Genes

19 pages, 4172 KiB

Open AccessArticle

Maternal Lineages from 10–11th Century Commoner Cemeteries of the Carpathian Basin

by Kitti Maár, Gergely I. B. Varga, Bence Kovács, Oszkár Schütz, Zoltán Maróti, Tibor Kalmár, Emil Nyerki, István Nagy, Dóra Latinovics, Balázs Tihanyi, Antónia Marcsik, György Pálfi, Zsolt Bernert, Zsolt Gallina, Sándor Varga, László Költő, István Raskó, Tibor Török and Endre Neparáczki

Genes 2021, 12(3), 460; https://doi.org/10.3390/genes12030460 - 23 Mar 2021

Cited by 12 | Viewed by 10507

Abstract

Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10–11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the [...] Read more.

Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10–11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10–11th century commoners most likely represent local populations of the Carpathian Basin, which admixed with the eastern immigrant groups (which included conquering Hungarians). Full article

(This article belongs to the Special Issue Ancient and Archaic Genomes)

► Show Figures

Figure 1

14 pages, 2595 KiB

Open AccessArticle

Appropriate Reference Genes for RT-qPCR Normalization in Various Organs of Anemone flaccida Fr. Schmidt at Different Growing Stages

by Zeying Zhao, Hanwen Zhou, Zhongnan Nie, Xuekui Wang, Biaobiao Luo, Zhijie Yi, Xinghua Li, Xuebo Hu and Tewu Yang

Genes 2021, 12(3), 459; https://doi.org/10.3390/genes12030459 - 23 Mar 2021

Cited by 5 | Viewed by 2737

Abstract

Anemone flaccida Fr. Schmidt is a traditional medicinal herb in southwestern China and has multiple pharmacological effects on bruise injuries and rheumatoid arthritis (RA). A new drug with a good curative effect on RA has recently been developed from the extract of A. [...] Read more.

Anemone flaccida Fr. Schmidt is a traditional medicinal herb in southwestern China and has multiple pharmacological effects on bruise injuries and rheumatoid arthritis (RA). A new drug with a good curative effect on RA has recently been developed from the extract of A. flaccida rhizomes, of which the main medicinal ingredients are triterpenoid saponins. Due to excessive exploitation, the wild population has been scarce and endangered in a few of its natural habitats and research on the cultivation of the plant commenced. Studies on the gene expressions related to the biosynthesis of triterpenoid saponins are not only helpful for understanding the effects of environmental factors on the medicinal ingredient accumulations but also necessary for monitoring the herb quality of the cultivated plants. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) as a sensitive and powerful technique has been widely used to detect gene expression across tissues in plants at different stages; however, its accuracy and reliability depend largely on the reference gene selection. In this study, the expressions of 10 candidate reference genes were evaluated in various organs of the wild and cultivated plants at different stages, using the algorithms of geNorm, NormFinder and BestKeeper, respectively. The purpose of this study was to identify the suitable reference genes for RT-qPCR detection in A. flaccida. The results showed that two reference genes were sufficient for RT-qPCR data normalization in A. flaccida. PUBQ and ETIF1a can be used as suitable reference genes in most organs at various stages because of their expression stabilitywhereas the PUBQ and EF1Α genes were desirable in the rhizomes of the plant at the vegetative stage. Full article

(This article belongs to the Section Plant Genetics and Genomics)

► Show Figures

Figure 1

5 pages, 191 KiB

Open AccessArticle

Phenotypic Presentations of Cystic Fibrosis in Children of African Descent

by Sophie Mayer Lacrosniere, Michele Gerardin, Laurence Le Clainche-Viala and Veronique Houdouin

Genes 2021, 12(3), 458; https://doi.org/10.3390/genes12030458 - 23 Mar 2021

Cited by 5 | Viewed by 1736

Abstract

The Robert Debre Pediatric Cystic Fibrosis (CF) centre, located in the North East of Paris, a multicultural area, is in charge of a cohort of around a hundred and sixty children diagnosed with CF. Between 2000 and 2019, the proportion of children of [...] Read more.

The Robert Debre Pediatric Cystic Fibrosis (CF) centre, located in the North East of Paris, a multicultural area, is in charge of a cohort of around a hundred and sixty children diagnosed with CF. Between 2000 and 2019, the proportion of children of African descent in this centre increased from 2% to 10%. We report the clinical features of 17 children of African descent diagnosed with CF: 4 (23%) were diagnosed after a meconium ileus, 14 (83%) had exocrine pancreatic insufficiency, and 7 (41%) had early Pseudomonas aeruginosa infection before the age of two. Even though the majority of patients were diagnosed through NBS, the twenty-nine-mutation testing kit proved less effective in non-Caucasian populations, with a false negative rate of 25% in this series. CF is definitely not solely a Caucasian disease and the literature reveals similar phenotypes in Caucasian and African people provided that they present the same CFTR mutations. Clinicians have to keep in mind that the diagnosis of CF in patients of African descent must be evoked in the case of symptoms and a sweat test must be performed, despite a negative result for NBS. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

21 pages, 3869 KiB

Open AccessEditor’s ChoiceArticle

Regulation of DNA (de)Methylation Positively Impacts Seed Germination during Seed Development under Heat Stress

by Jaiana Malabarba, David Windels, Wenjia Xu and Jerome Verdier

Genes 2021, 12(3), 457; https://doi.org/10.3390/genes12030457 - 23 Mar 2021

Cited by 20 | Viewed by 4481

Abstract

Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling, and the acquisition of germination capacity, desiccation tolerance, longevity, and dormancy. Heat stress can negatively impact these processes and upon the increase of global mean temperatures, global [...] Read more.

Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling, and the acquisition of germination capacity, desiccation tolerance, longevity, and dormancy. Heat stress can negatively impact these processes and upon the increase of global mean temperatures, global food security is threatened. Here, we explored the impact of heat stress on seed physiology, morphology, gene expression, and methylation on three stages of seed development. Notably, Arabidopsis Col-0 plants under heat stress presented a decrease in germination capacity as well as a decrease in longevity. We observed that upon mild stress, gene expression and DNA methylation were moderately affected. Nevertheless, upon severe heat stress during seed development, gene expression was intensively modified, promoting heat stress response mechanisms including the activation of the ABA pathway. By analyzing candidate epigenetic markers using the mutants’ physiological assays, we observed that the lack of DNA demethylation by the ROS1 gene impaired seed germination by affecting germination-related gene expression. On the other hand, we also observed that upon severe stress, a large proportion of differentially methylated regions (DMRs) were located in the promoters and gene sequences of germination-related genes. To conclude, our results indicate that DNA (de)methylation could be a key regulatory process to ensure proper seed germination of seeds produced under heat stress. Full article

(This article belongs to the Special Issue Seeds and Epigenetics)

► Show Figures

Graphical abstract

20 pages, 1481 KiB

Open AccessArticle

Identification of Genomic Regions Associated with Concentrations of Milk Fat, Protein, Urea and Efficiency of Crude Protein Utilization in Grazing Dairy Cows

by Hewa Bahithige Pavithra Chathurangi Ariyarathne, Martin Correa-Luna, Hugh Thomas Blair, Dorian John Garrick and Nicolas Lopez-Villalobos

Genes 2021, 12(3), 456; https://doi.org/10.3390/genes12030456 - 23 Mar 2021

Cited by 13 | Viewed by 2795

Abstract

The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using [...] Read more.

The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10⁻⁶ were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows. Full article

(This article belongs to the Section Animal Genetics and Genomics)

► Show Figures

Figure 1

19 pages, 2388 KiB

Open AccessReview

Long Non-Coding RNAs in Multidrug Resistance of Glioblastoma

by Parvaneh Mahinfar, Behzad Baradaran, Sadaf Davoudian, Fatemeh Vahidian, William Chi-Shing Cho and Behzad Mansoori

Genes 2021, 12(3), 455; https://doi.org/10.3390/genes12030455 - 23 Mar 2021

Cited by 14 | Viewed by 3011

Abstract

Glioblastoma, also known as glioblastoma multiforme, is the most aggressive brain tumor in adults. Despite the huge advance in developing novel therapeutic strategies for patients with glioblastoma, the appearance of multidrug resistance (MDR) against the common chemotherapeutic agents, including temozolomide, is considered as [...] Read more.

Glioblastoma, also known as glioblastoma multiforme, is the most aggressive brain tumor in adults. Despite the huge advance in developing novel therapeutic strategies for patients with glioblastoma, the appearance of multidrug resistance (MDR) against the common chemotherapeutic agents, including temozolomide, is considered as one of the important causes for the failure of glioblastoma treatment. On the other hand, recent studies have demonstrated the critical roles of long non-coding RNAs (lncRNAs), particularly in the development of MDR in glioblastoma. Therefore, this article aimed to review lncRNA’s contribution to the regulation of MDR and elucidate the underlying mechanisms in glioblastoma, which will open up new lines of inquiry in the treatment of glioblastoma. Full article

(This article belongs to the Special Issue Transcription Factors in Cancer Progression)

► Show Figures

Figure 1

13 pages, 2036 KiB

Open AccessArticle

Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing

by Xuefeng Shen, Ran Li, Haixia Li, Yu Gao, Hui Chen, Ning Qu, Dan Peng, Riga Wu and Hongyu Sun

Genes 2021, 12(3), 454; https://doi.org/10.3390/genes12030454 - 22 Mar 2021

Cited by 9 | Viewed by 3017

Abstract

Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on [...] Read more.

Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on massively parallel sequencing (MPS), this study used a widely-accepted forensic multiplex assay system to evaluate the effect of noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers. Using a ForenSeq DNA Signature Prep Kit, NIPPT was performed in 17 real parentage cases with monovular unborn fetuses at 7 to 24 gestational weeks. Different analytical strategies for the identification of paternally inherited allele (PIA) were developed to deal with SNPs and STRs. Combined paternity index (CPI) for 17 real trios as well as 272 unrelated trios was calculated. With the combination of SNPs and A-STRs, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17), and 94.12% (16/17) of real trios could be accurately determined when the likelihood ratio (LR) threshold for paternity inclusion was set to 10,000, 1000, 100, and 10, respectively. This reveals that simultaneous surveys of SNP and STR markers included in the ForenSeq DNA Signature Prep Kit offer a promising method for NIPPT using MPS technology. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

► Show Figures

Figure 1

8 pages, 547 KiB

Open AccessReview

Modulation of Ion Transport to Restore Airway Hydration in Cystic Fibrosis

by James A. Reihill, Lisa E. J. Douglas and S. Lorraine Martin

Genes 2021, 12(3), 453; https://doi.org/10.3390/genes12030453 - 22 Mar 2021

Cited by 7 | Viewed by 3257

Abstract

Cystic fibrosis (CF) is a life-limiting genetic disorder caused by loss-of-function mutations in the gene which codes for the CF transmembrane conductance regulator (CFTR) Cl⁻ channel. Loss of Cl⁻ secretion across the apical membrane of airway lining epithelial cells results in [...] Read more.

Cystic fibrosis (CF) is a life-limiting genetic disorder caused by loss-of-function mutations in the gene which codes for the CF transmembrane conductance regulator (CFTR) Cl⁻ channel. Loss of Cl⁻ secretion across the apical membrane of airway lining epithelial cells results in dehydration of the airway surface liquid (ASL) layer which impairs mucociliary clearance (MCC), and as a consequence promotes bacterial infection and inflammation of the airways. Interventions that restore airway hydration are known to improve MCC. Here we review the ion channels present at the luminal surface of airway epithelial cells that may be targeted to improve airway hydration and MCC in CF airways. Full article

(This article belongs to the Special Issue Phenotypic Variability of Cystic Fibrosis: New Challenges)

► Show Figures

Figure 1

8 pages, 1223 KiB

Open AccessCase Report

Shukla-Vernon Syndrome: A Second Family with a Novel Variant in the BCORL1 Gene

by Babylakshmi Muthusamy, Anikha Bellad, Satish Chandra Girimaji and Akhilesh Pandey

Genes 2021, 12(3), 452; https://doi.org/10.3390/genes12030452 - 22 Mar 2021

Cited by 5 | Viewed by 4022

Abstract

Shukla-Vernon syndrome (SHUVER) is an extremely rare neurodevelopmental disorder characterized by global developmental delay, intellectual disability, behavioral anomalies, and dysmorphic features. Pathogenic variants in the BCORL1 gene have been identified as the molecular cause for this disorder. The BCORL1 gene encodes for BCL-6 [...] Read more.

Shukla-Vernon syndrome (SHUVER) is an extremely rare neurodevelopmental disorder characterized by global developmental delay, intellectual disability, behavioral anomalies, and dysmorphic features. Pathogenic variants in the BCORL1 gene have been identified as the molecular cause for this disorder. The BCORL1 gene encodes for BCL-6 corepressor-like protein 1, a transcriptional corepressor that is an integral component of protein complexes involved in transcription repression. In this study, we report an Indian family with two male siblings with features of Shukla-Vernon syndrome. The patients exhibited global developmental delay, intellectual disability, kyphosis, seizures, and dysmorphic features including bushy prominent eyebrows with synophrys, sharp beaked prominent nose, protuberant lower jaw, squint, and hypoplastic ears with fused ear lobes. No behavioral abnormalities were observed. Whole exome sequencing revealed a novel potentially pathogenic arginine to cysteine substitution (p.Arg1265Cys) in the BCORL1 protein. This is the second report of Shukla-Vernon syndrome with a novel missense variant in the BCORL1 gene. Our study confirms and expands the phenotypes and genotypes described previously for this syndrome and should aid in diagnosis and genetic counselling of patients and their families. Full article

(This article belongs to the Special Issue Genetics and Genomics of Intellectual Disability)

► Show Figures

Figure 1

10 pages, 988 KiB

Open AccessArticle

The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein

by Pablo Mier and Miguel A. Andrade-Navarro

Genes 2021, 12(3), 451; https://doi.org/10.3390/genes12030451 - 22 Mar 2021

Cited by 3 | Viewed by 2590

Abstract

Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence [...] Read more.

Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence in eukaryotes. Studying their conservation could help provide hypotheses about their function. To obtain the appropriate evolutionary focus for this rapidly evolving feature, here we study the conservation of LCRs in bacterial strains and compare their high variability to the closeness of the strains. For this, we selected 20 taxonomically diverse bacterial species and obtained the completely sequenced proteomes of two strains per species. We calculated all orthologous pairs for each of the 20 strain pairs. Per orthologous pair, we computed the conservation of two types of LCRs: compositionally biased regions (CBRs) and homorepeats (polyX). Our results show that, in bacteria, Q-rich CBRs are the most conserved, while A-rich CBRs and polyA are the most variable. LCRs have generally higher conservation when comparing pathogenic strains. However, this result depends on protein subcellular location: LCRs accumulate in extracellular and outer membrane proteins, with conservation increased in the extracellular proteins of pathogens, and decreased for polyX in the outer membrane proteins of pathogens. We conclude that these dependencies support the functional importance of LCRs in host–pathogen interactions. Full article

(This article belongs to the Special Issue Trends and Future Perspectives in Genome Annotation)

► Show Figures

Figure 1

11 pages, 2248 KiB

Open AccessArticle

A Resource for the Network Representation of Cell Perturbations Caused by SARS-CoV-2 Infection

by Livia Perfetto, Elisa Micarelli, Marta Iannuccelli, Prisca Lo Surdo, Giulio Giuliani, Sara Latini, Giusj Monia Pugliese, Giorgia Massacci, Simone Vumbaca, Federica Riccio, Claudia Fuoco, Serena Paoluzi, Luisa Castagnoli, Gianni Cesareni, Luana Licata and Francesca Sacco

Genes 2021, 12(3), 450; https://doi.org/10.3390/genes12030450 - 22 Mar 2021

Cited by 6 | Viewed by 2793

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has caused more than 2.3 million casualties worldwide and the lack of effective treatments is a major health concern. The development of targeted drugs is held back due to a limited understanding of the molecular mechanisms underlying [...] Read more.

The coronavirus disease 2019 (COVID-19) pandemic has caused more than 2.3 million casualties worldwide and the lack of effective treatments is a major health concern. The development of targeted drugs is held back due to a limited understanding of the molecular mechanisms underlying the perturbation of cell physiology observed after viral infection. Recently, several approaches, aimed at identifying cellular proteins that may contribute to COVID-19 pathology, have been reported. Albeit valuable, this information offers limited mechanistic insight as these efforts have produced long lists of cellular proteins, the majority of which are not annotated to any cellular pathway. We have embarked in a project aimed at bridging this mechanistic gap by developing a new bioinformatic approach to estimate the functional distance between a subset of proteins and a list of pathways. A comprehensive literature search allowed us to annotate, in the SIGNOR 2.0 resource, causal information underlying the main molecular mechanisms through which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses affect the host–cell physiology. Next, we developed a new strategy that enabled us to link SARS-CoV-2 interacting proteins to cellular phenotypes via paths of causal relationships. Remarkably, the extensive information about inhibitors of signaling proteins annotated in SIGNOR 2.0 makes it possible to formulate new potential therapeutic strategies. The proposed approach, which is generally applicable, generated a literature-based causal network that can be used as a framework to formulate informed mechanistic hypotheses on COVID-19 etiology and pathology. Full article

(This article belongs to the Special Issue COVID-19 and Molecular Genetics)

► Show Figures

Figure 1

15 pages, 3312 KiB

Open AccessArticle

Pilot Study to Detect Genes Involved in DNA Damage and Cancer in Humans: Potential Biomarkers of Exposure to E-Cigarette Aerosols

by Samera H. Hamad, Marielle C. Brinkman, Yi-Hsuan Tsai, Namya Mellouk, Kandice Cross, Ilona Jaspers, Pamela I. Clark and Courtney A. Granville

Genes 2021, 12(3), 448; https://doi.org/10.3390/genes12030448 - 22 Mar 2021

Cited by 9 | Viewed by 4495

Abstract

There is a paucity of data on how gene expression enables identification of individuals who are at risk of exposure to carcinogens from e-cigarette (e-cig) vaping; and how human vaping behaviors modify these exposures. This pilot study aimed to identify genes regulated from [...] Read more.

There is a paucity of data on how gene expression enables identification of individuals who are at risk of exposure to carcinogens from e-cigarette (e-cig) vaping; and how human vaping behaviors modify these exposures. This pilot study aimed to identify genes regulated from acute exposure to e-cig using RT-qPCR. Three subjects (2M and 1F) made three visits to the lab (n_TOT = 9 visits); buccal and blood samples were collected before and immediately after scripted vaping 20 puffs (n_TOT = 18 samples); vaping topography data were collected in each session. Subjects used their own e-cig containing 50:50 propylene glycol (PG):vegetable glycerine (VG) +3–6 mg/mL nicotine. The tumor suppressor TP53 was significantly upregulated in buccal samples. TP53 expression was puff volume and flow rate dependent in both tissues. In blood, the significant downregulation of N-methylpurine DNA glycosylase (MPG), a base excision repair gene, was consistent across all subjects. In addition to DNA repair pathway, cell cycle and cancer pathways were the most enriched pathways in buccal and blood samples, respectively. This pilot study demonstrates that vaping 20 puffs significantly alters expression of TP53 in human tissues; vaping behavior is an important modifier of this response. A larger study is needed to confirm these relationships. Full article

(This article belongs to the Special Issue Molecular Biomarkers of Pulmonary Diseases)

► Show Figures

Graphical abstract

18 pages, 4921 KiB

Open AccessArticle

Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses

by Hansen Fu, Tuo Zeng, Yangyang Zhao, Tingting Luo, Huijie Deng, Chenwei Meng, Jing Luo and Caiyun Wang

Genes 2021, 12(3), 449; https://doi.org/10.3390/genes12030449 - 21 Mar 2021

Cited by 9 | Viewed by 3212

Abstract

Green chrysanthemums are difficult to breed but have high commercial value. The molecular basis for the green petal color in chrysanthemum is not fully understood. This was investigated in the present study by RNA sequencing analysis of white and green ray florets collected [...] Read more.

Green chrysanthemums are difficult to breed but have high commercial value. The molecular basis for the green petal color in chrysanthemum is not fully understood. This was investigated in the present study by RNA sequencing analysis of white and green ray florets collected at three stages of flower development from the F₁ progeny of the cross between Chrysanthemum × morifolium “Lüdingdang” with green-petaled flowers and Chrysanthemum vistitum with white-petaled flowers. The chlorophyll content was higher and chloroplast degradation was slower in green pools than in white pools at each developmental stage. Transcriptome analysis revealed that genes that were differentially expressed between the two pools were enriched in pathways related to chlorophyll metabolism and photosynthesis. We identified the transcription factor genes CmCOLa, CmCOLb, CmERF, and CmbHLH as regulators of the green flower color in chrysanthemum by differential expression analysis and weighted gene co-expression network analysis. These findings can guide future efforts to improve the color palette of chrysanthemum flowers through genetic engineering. Full article

(This article belongs to the Section Plant Genetics and Genomics)

► Show Figures

Figure 1

21 pages, 5369 KiB

Open AccessArticle

A Bibliometric and Citation Network Analysis of Myopia Genetics

by Cristina Alvarez-Peregrina, Clara Martinez-Perez, Cesar Villa-Collar and Miguel Ángel Sánchez-Tena

Genes 2021, 12(3), 447; https://doi.org/10.3390/genes12030447 - 21 Mar 2021

Cited by 12 | Viewed by 3073

Abstract

Background: To aim of the study was describe the growth of publications on genetic myopia and understand the current research landscape through the analysis of citation networks, as well as determining the different research areas and the most cited publications. Methods: The Web [...] Read more.

Background: To aim of the study was describe the growth of publications on genetic myopia and understand the current research landscape through the analysis of citation networks, as well as determining the different research areas and the most cited publications. Methods: The Web of Science database was used to perform the publication search, looking for the terms “genetic*” AND “myopia” within the period between 2009 and October 2020. The CitNetExplorer and CiteSpace software were then used to conduct the publication analysis. To obtain the graphics, the VOSviewer software was used. Results: A total of 721 publications were found with 2999 citations generated within the network. The year 2019 was singled out as a “key year”, taking into account the number of publications that emerged in that year and given that in 2019, 200 loci associated with refractive errors and myopia were found, which is considered to be great progress. The most widely cited publication was “Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia”, an article by Verhoeven et al., which was published in 2013. By using the clustering function, we were able to establish three groups that encompassed the different research areas within this field: heritability rate of myopia and its possible association with environmental factors, retinal syndromes associated with myopia and the genetic factors that control and influence axial growth of the eye. Conclusions: The citation network offers a comprehensive and objective analysis of the main papers that address genetic myopia. Full article

(This article belongs to the Special Issue Genetics in Ophthalmology)

► Show Figures

Figure 1

16 pages, 1546 KiB

Open AccessEditor’s ChoiceReview

The PARP Way to Epigenetic Changes

by Simone Ummarino, Clinton Hausman and Annalisa Di Ruscio

Genes 2021, 12(3), 446; https://doi.org/10.3390/genes12030446 - 20 Mar 2021

Cited by 23 | Viewed by 4328

Abstract

ADP-ribosylation, is a reversible post-translational modification implicated in major biological functions. Poly ADP-ribose polymerases (PARP) are specialized enzymes that catalyze the addition of ADP ribose units from “nicotinamide adenine dinucleotide-donor molecules” to their target substrates. This reaction known as PARylation modulates essential cellular [...] Read more.

ADP-ribosylation, is a reversible post-translational modification implicated in major biological functions. Poly ADP-ribose polymerases (PARP) are specialized enzymes that catalyze the addition of ADP ribose units from “nicotinamide adenine dinucleotide-donor molecules” to their target substrates. This reaction known as PARylation modulates essential cellular processes including DNA damage response, chromatin remodeling, DNA methylation and gene expression. Herein, we discuss emerging roles of PARP1 in chromatin remodeling and epigenetic regulation, focusing on its therapeutic implications for cancer treatment and beyond. Full article

(This article belongs to the Special Issue Advances in Tumor Epigenetics Research)

► Show Figures

Figure 1

24 pages, 1008 KiB

Open AccessEditor’s ChoiceReview

Decipher the Glioblastoma Microenvironment: The First Milestone for New Groundbreaking Therapeutic Strategies

by Giuseppe Nicolò Fanelli, Dario Grassini, Valerio Ortenzi, Francesco Pasqualetti, Nicola Montemurro, Paolo Perrini, Antonio Giuseppe Naccarato and Cristian Scatena

Genes 2021, 12(3), 445; https://doi.org/10.3390/genes12030445 - 20 Mar 2021

Cited by 65 | Viewed by 5861

Abstract

Glioblastoma (GBM) is the most common primary malignant brain tumour in adults. Despite the combination of novel therapeutical approaches, it remains a deadly malignancy with an abysmal prognosis. GBM is a polymorphic tumour from both molecular and histological points of view. It consists [...] Read more.

Glioblastoma (GBM) is the most common primary malignant brain tumour in adults. Despite the combination of novel therapeutical approaches, it remains a deadly malignancy with an abysmal prognosis. GBM is a polymorphic tumour from both molecular and histological points of view. It consists of different malignant cells and various stromal cells, contributing to tumour initiation, progression, and treatment response. GBM’s microenvironment is multifaceted and is made up of soluble factors, extracellular matrix components, tissue-resident cell types (e.g., neurons, astrocytes, endothelial cells, pericytes, and fibroblasts) together with resident (e.g., microglia) or recruited (e.g., bone marrow-derived macrophages) immune cells. These latter constitute the so-called immune microenvironment, accounting for a substantial GBM’s tumour volume. Despite the abundance of immune cells, an intense state of tumour immunosuppression is promoted and developed; this represents the significant challenge for cancer cells’ immune-mediated destruction. Though literature data suggest that distinct GBM’s subtypes harbour differences in their microenvironment, its role in treatment response remains obscure. However, an in-depth investigation of GBM’s microenvironment may lead to novel therapeutic opportunities to improve patients’ outcomes. This review will elucidate the GBM’s microenvironment composition, highlighting the current state of the art in immunotherapy approaches. We will focus on novel strategies of active and passive immunotherapies, including vaccination, gene therapy, checkpoint blockade, and adoptive T-cell therapies. Full article

(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)

► Show Figures

Figure 1

20 pages, 1107 KiB

Open AccessArticle

Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity

by Amanda T. S. Albanaz, Evgeny S. Gerasimov, Jeffrey J. Shaw, Jovana Sádlová, Julius Lukeš, Petr Volf, Fred R. Opperdoes, Alexei Y. Kostygov, Anzhelika Butenko and Vyacheslav Yurchenko

Genes 2021, 12(3), 444; https://doi.org/10.3390/genes12030444 - 20 Mar 2021

Cited by 10 | Viewed by 3591

Abstract

While numerous genomes of Leishmania spp. have been sequenced and analyzed, an understanding of the evolutionary history of these organisms remains limited due to the unavailability of the sequence data for their closest known relatives, Endotrypanum and Porcisia spp., infecting sloths and porcupines. [...] Read more.

While numerous genomes of Leishmania spp. have been sequenced and analyzed, an understanding of the evolutionary history of these organisms remains limited due to the unavailability of the sequence data for their closest known relatives, Endotrypanum and Porcisia spp., infecting sloths and porcupines. We have sequenced and analyzed genomes of three members of this clade in order to fill this gap. Their comparative analyses revealed only minute differences from Leishmaniamajor genome in terms of metabolic capacities. We also documented that the number of genes under positive selection on the Endotrypanum/Porcisia branch is rather small, with the flagellum-related group of genes being over-represented. Most significantly, the analysis of gene family evolution revealed a substantially reduced repertoire of surface proteins, such as amastins and biopterin transporters BT1 in the Endotrypanum/Porcisia species when compared to amastigote-dwelling Leishmania. This reduction was especially pronounced for δ-amastins, a subfamily of cell surface proteins crucial in the propagation of Leishmania amastigotes inside vertebrate macrophages and, apparently, dispensable for Endotrypanum/Porcisia, which do not infect such cells. Full article

(This article belongs to the Special Issue Genetics and Genomics of Leishmania)

► Show Figures

Figure 1

12 pages, 275 KiB

Open AccessArticle

The Impact of Complement Genes on the Risk of Late-Onset Alzheimer’s Disease

by Sarah M. Carpanini, Janet C. Harwood, Emily Baker, Megan Torvell, The GERAD1 Consortium, Rebecca Sims, Julie Williams and B. Paul Morgan

Genes 2021, 12(3), 443; https://doi.org/10.3390/genes12030443 - 20 Mar 2021

Cited by 14 | Viewed by 3348

Abstract

Late-onset Alzheimer’s disease (LOAD), the most common cause of dementia, and a huge global health challenge, is a neurodegenerative disease of uncertain aetiology. To deliver effective diagnostics and therapeutics, understanding the molecular basis of the disease is essential. Contemporary large genome-wide association studies [...] Read more.

Late-onset Alzheimer’s disease (LOAD), the most common cause of dementia, and a huge global health challenge, is a neurodegenerative disease of uncertain aetiology. To deliver effective diagnostics and therapeutics, understanding the molecular basis of the disease is essential. Contemporary large genome-wide association studies (GWAS) have identified over seventy novel genetic susceptibility loci for LOAD. Most are implicated in microglial or inflammatory pathways, bringing inflammation to the fore as a candidate pathological pathway. Among the most significant GWAS hits are three complement genes: CLU, encoding the fluid-phase complement inhibitor clusterin; CR1 encoding complement receptor 1 (CR1); and recently, C1S encoding the complement enzyme C1s. Complement activation is a critical driver of inflammation; changes in complement genes may impact risk by altering the inflammatory status in the brain. To assess complement gene association with LOAD risk, we manually created a comprehensive complement gene list and tested these in gene-set analysis with LOAD summary statistics. We confirmed associations of CLU and CR1 genes with LOAD but showed no significant associations for the complement gene-set when excluding CLU and CR1. No significant association with other complement genes, including C1S, was seen in the IGAP dataset; however, these may emerge from larger datasets. Full article

(This article belongs to the Special Issue Genetics of Alzheimer’s Disease)

11 pages, 988 KiB

Open AccessReview

Spatial Organization and Coordination of the Plant Circadian System

by Maria A. Nohales

Genes 2021, 12(3), 442; https://doi.org/10.3390/genes12030442 - 20 Mar 2021

Cited by 9 | Viewed by 3433

Abstract

The plant circadian clock has a pervasive influence on many aspects of plant biology and is proposed to function as a developmental manager. To do so, the circadian oscillator needs to be able to integrate a multiplicity of environmental signals and coordinate an [...] Read more.

The plant circadian clock has a pervasive influence on many aspects of plant biology and is proposed to function as a developmental manager. To do so, the circadian oscillator needs to be able to integrate a multiplicity of environmental signals and coordinate an extensive and diverse repertoire of endogenous rhythms accordingly. Recent studies on tissue-specific characteristics and spatial structure of the plant circadian clock suggest that such plasticity may be achieved through the function of distinct oscillators, which sense the environment locally and are then coordinated across the plant through both intercellular coupling and long-distance communication. This review summarizes the current knowledge on tissue-specific features of the clock in plants and their spatial organization and synchronization at the organismal level. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Circadian Clock Function in Plants)

► Show Figures

Figure 1

13 pages, 4081 KiB

Open AccessArticle

DNA Methylation at ATP11A cg11702988 Is a Biomarker of Lung Disease Severity in Cystic Fibrosis: A Longitudinal Study

by Fanny Pineau, Davide Caimmi, Sylvie Taviaux, Maurane Reveil, Laura Brosseau, Isabelle Rivals, Margot Drevait, Isabelle Vachier, Mireille Claustres, Raphaël Chiron and Albertina De Sario

Genes 2021, 12(3), 441; https://doi.org/10.3390/genes12030441 - 19 Mar 2021

Cited by 3 | Viewed by 2159

Abstract

Cystic fibrosis (CF) is a chronic genetic disease that mainly affects the respiratory and gastrointestinal systems. No curative treatments are available, but the follow-up in specialized centers has greatly improved the patient life expectancy. Robust biomarkers are required to monitor the disease, guide [...] Read more.

Cystic fibrosis (CF) is a chronic genetic disease that mainly affects the respiratory and gastrointestinal systems. No curative treatments are available, but the follow-up in specialized centers has greatly improved the patient life expectancy. Robust biomarkers are required to monitor the disease, guide treatments, stratify patients, and provide outcome measures in clinical trials. In the present study, we outline a strategy to select putative DNA methylation biomarkers of lung disease severity in cystic fibrosis patients. In the discovery step, we selected seven potential biomarkers using a genome-wide DNA methylation dataset that we generated in nasal epithelial samples from the MethylCF cohort. In the replication step, we assessed the same biomarkers using sputum cell samples from the MethylBiomark cohort. Of interest, DNA methylation at the cg11702988 site (ATP11A gene) positively correlated with lung function and BMI, and negatively correlated with lung disease severity, P. aeruginosa chronic infection, and the number of exacerbations. These results were replicated in prospective sputum samples collected at four time points within an 18-month period and longitudinally. To conclude, (i) we identified a DNA methylation biomarker that correlates with CF severity, (ii) we provided a method to easily assess this biomarker, and (iii) we carried out the first longitudinal analysis of DNA methylation in CF patients. This new epigenetic biomarker could be used to stratify CF patients in clinical trials. Full article

(This article belongs to the Special Issue Phenotypic Variability of Cystic Fibrosis: New Challenges)

► Show Figures

Figure 1

15 pages, 5113 KiB

Open AccessReview

The Important Role of N6-methyladenosine RNA Modification in Non-Small Cell Lung Cancer

by Yue Cheng, Meiqi Wang, Junliang Zhou, Huanhuan Dong, Shuqing Wang and Hui Xu

Genes 2021, 12(3), 440; https://doi.org/10.3390/genes12030440 - 19 Mar 2021

Cited by 15 | Viewed by 2624

Abstract

N6-methyladenosine (m⁶A) is one of the most prevalent epigenetic modifications of eukaryotic RNA. The m⁶A modification is a dynamic and reversible process, regulated by three kinds of regulator, including m⁶A methyltransferases, demethylases and m⁶A-binding proteins, [...] Read more.

N6-methyladenosine (m⁶A) is one of the most prevalent epigenetic modifications of eukaryotic RNA. The m⁶A modification is a dynamic and reversible process, regulated by three kinds of regulator, including m⁶A methyltransferases, demethylases and m⁶A-binding proteins, and this modification plays a vital role in many diseases, especially in cancers. Accumulated evidence has proven that this modification has a significant effect on cellular biological functions and cancer progression; however, little is known about the effects of the m⁶A modification in non-small cell lung cancer (NSCLC). In this review, we summarized how various m⁶A regulators modulate m⁶A RNA metabolism and demonstrated the effect of m⁶A modification on the progression and cellular biological functions of NSCLC. We also discussed how m⁶A modification affects the treatment, drug resistance, diagnosis and prognosis of NSCLC patients. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

► Show Figures

Figure 1

21 pages, 7042 KiB

Open AccessArticle

Characterization of Two Ethephon-Induced IDA-Like Genes from Mango, and Elucidation of Their Involvement in Regulating Organ Abscission

by Avinash Chandra Rai, Eyal Halon, Hanita Zemach, Tali Zviran, Isaac Sisai, Sonia Philosoph-Hadas, Shimon Meir, Yuval Cohen and Vered Irihimovitch

Genes 2021, 12(3), 439; https://doi.org/10.3390/genes12030439 - 19 Mar 2021

Cited by 8 | Viewed by 2826

Abstract

In mango (Mangifera indica L.), fruitlet abscission limits productivity. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide acts as a key component controlling abscission events in Arabidopsis. IDA-like peptides may assume similar roles in fruit trees. In this study, we isolated two mango [...] Read more.

In mango (Mangifera indica L.), fruitlet abscission limits productivity. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide acts as a key component controlling abscission events in Arabidopsis. IDA-like peptides may assume similar roles in fruit trees. In this study, we isolated two mango IDA-like encoding-genes, MiIDA1 and MiIDA2. We used mango fruitlet-bearing explants and fruitlet-bearing trees, in which fruitlets abscission was induced using ethephon. We monitored the expression profiles of the two MiIDA-like genes in control and treated fruitlet abscission zones (AZs). In both systems, qRT-PCR showed that, within 24 h, both MiIDA-like genes were induced by ethephon, and that changes in their expression profiles were associated with upregulation of different ethylene signaling-related and cell-wall modifying genes. Furthermore, ectopic expression of both genes in Arabidopsis promoted floral-organ abscission, and was accompanied by an early increase in the cytosolic pH of floral AZ cells—a phenomenon known to be linked with abscission, and by activation of cell separation in vestigial AZs. Finally, overexpression of both genes in an Atida mutant restored its abscission ability. Our results suggest roles for MiIDA1 and MiIDA2 in affecting mango fruitlet abscission. Based on our results, we propose new possible modes of action for IDA-like proteins in regulating organ abscission. Full article

(This article belongs to the Special Issue Genetic Basis and Physiology of Fruit Ripening and Abscission)

► Show Figures

Figure 1

21 pages, 3453 KiB

Open AccessReview

In Vitro Plant Regeneration in Conifers: The Role of WOX and KNOX Gene Families

by Natalia Bueno, Candela Cuesta, María Luz Centeno, Ricardo J. Ordás and José M. Alvarez

Genes 2021, 12(3), 438; https://doi.org/10.3390/genes12030438 - 19 Mar 2021

Cited by 14 | Viewed by 3796

Abstract

Conifers are a group of woody plants with an enormous economic and ecological importance. Breeding programs are necessary to select superior varieties for planting, but they have many limitations due to the biological characteristics of conifers. Somatic embryogenesis (SE) and de novo organogenesis [...] Read more.

Conifers are a group of woody plants with an enormous economic and ecological importance. Breeding programs are necessary to select superior varieties for planting, but they have many limitations due to the biological characteristics of conifers. Somatic embryogenesis (SE) and de novo organogenesis (DNO) from in vitro cultured tissues are two ways of plant mass propagation that help to overcome this problem. Although both processes are difficult to achieve in conifers, they offer advantages like a great efficiency, the possibilities to cryopreserve the embryogenic lines, and the ability of multiplying adult trees (the main bottleneck in conifer cloning) through DNO. Moreover, SE and DNO represent appropriate experimental systems to study the molecular bases of developmental processes in conifers such as embryogenesis and shoot apical meristem (SAM) establishment. Some of the key genes regulating these processes belong to the WOX and KNOX homeobox gene families, whose function has been widely described in Arabidopsis thaliana. The sequences and roles of these genes in conifers are similar to those found in angiosperms, but some particularities exist, like the presence of WOXX, a gene that putatively participates in the establishment of SAM in somatic embryos and plantlets of Pinus pinaster. Full article

(This article belongs to the Special Issue Genetics of Plant Organogenesis and Tissue Regeneration)

► Show Figures

Figure 1

14 pages, 2732 KiB

Open AccessArticle

Genetic Variation of the Serine Acetyltransferase Gene Family for Sulfur Assimilation in Maize

by Zhixuan Zhao, Shuai Li, Chen Ji, Yong Zhou, Changsheng Li and Wenqin Wang

Genes 2021, 12(3), 437; https://doi.org/10.3390/genes12030437 - 19 Mar 2021

Viewed by 2514

Abstract

Improving sulfur assimilation in maize kernels is essential due to humans and animals’ inability to synthesize methionine. Serine acetyltransferase (SAT) is a critical enzyme that controls cystine biosynthesis in plants. In this study, all SAT gene members were genome-wide characterized by using a [...] Read more.

Improving sulfur assimilation in maize kernels is essential due to humans and animals’ inability to synthesize methionine. Serine acetyltransferase (SAT) is a critical enzyme that controls cystine biosynthesis in plants. In this study, all SAT gene members were genome-wide characterized by using a sequence homology search. The RNA-seq quantification indicates that they are highly expressed in leaves, other than root and seeds, consistent with their biological functions in sulfur assimilation. With the recently released 25 genomes of nested association mapping (NAM) founders representing the diverse maize stock, we had the opportunity to investigate the SAT genetic variation comprehensively. The abundant transposon insertions into SAT genes indicate their driving power in terms of gene structure and genome evolution. We found that the transposon insertion into exons could change SAT gene transcription, whereas there was no significant correlation between transposable element (TE) insertion into introns and their gene expression, indicating that other regulatory elements such as promoters could also be involved. Understanding the SAT gene structure, gene expression and genetic variation involved in natural selection and species adaption could precisely guide genetic engineering to manipulate sulfur assimilation in maize and to improve nutritional quality. Full article

(This article belongs to the Special Issue Transposable Elements in Plant Genomes)

► Show Figures

Figure 1

15 pages, 1962 KiB

Open AccessArticle

Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania)

by Alexandra Gînguță, Ioana Rusu, Cristina Mircea, Adrian Ioniță, Horia L. Banciu and Beatrice Kelemen

Genes 2021, 12(3), 436; https://doi.org/10.3390/genes12030436 - 19 Mar 2021

Cited by 2 | Viewed by 9390

Abstract

The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such [...] Read more.

The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe. Full article

(This article belongs to the Special Issue Ancient and Archaic Genomes)

► Show Figures

Figure 1

15 pages, 2016 KiB

Open AccessArticle

Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species

by Thijs M. P. Bal, Alejandro Llanos-Garrido, Anurag Chaturvedi, Io Verdonck, Bart Hellemans and Joost A. M. Raeymaekers

Genes 2021, 12(3), 435; https://doi.org/10.3390/genes12030435 - 18 Mar 2021

Cited by 5 | Viewed by 2781

Abstract

There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address [...] Read more.

There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context. Full article

(This article belongs to the Special Issue Evolutionary Dynamics of Wild Populations)

► Show Figures

Figure 1

16 pages, 2618 KiB

Open AccessArticle

Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis

by Longjie Ni, Zhiquan Wang, Jinbo Guo, Xiaoxiao Pei, Liangqin Liu, Huogen Li, Haiyan Yuan and Chunsun Gu

Genes 2021, 12(3), 434; https://doi.org/10.3390/genes12030434 - 18 Mar 2021

Cited by 16 | Viewed by 3174

Abstract

Iris lactea var. chinensis (I. lactea var. chinensis) is a perennial herb halophyte with salt and drought tolerance. In this study, full-length transcripts of I. lactea var. chinensis were sequenced using the PacBio RSII sequencing platform. Moreover, the transcriptome was investigated [...] Read more.

Iris lactea var. chinensis (I. lactea var. chinensis) is a perennial herb halophyte with salt and drought tolerance. In this study, full-length transcripts of I. lactea var. chinensis were sequenced using the PacBio RSII sequencing platform. Moreover, the transcriptome was investigated under NaCl or polyethylene glycol (PEG) stress. Approximately 30.89 G subreads were generated and 31,195 unigenes were obtained by clustering the same isoforms by the PacBio RSII platform. A total of 15,466 differentially expressed genes (DEGs) were obtained under the two stresses using the Illumina platform. Among them, 9266 and 8390 DEGs were obtained under high concentrations of NaCl and PEG, respectively. In total, 3897 DEGs with the same expression pattern under the two stresses were obtained. The transcriptome expression profiles of I. lactea var. chinensis under NaCl or PEG stress obtained in this study may provide a resource for the same and different response mechanisms against different types of abiotic stress. Furthermore, the stress-related genes found in this study can provide data for future molecular breeding. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Changes in Plant Response to Abiotic Stress)

► Show Figures

Figure 1

13 pages, 1643 KiB

Open AccessArticle

Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

by Seyed Mohammad Ghoreishifar, Christina Marie Rochus, Sima Moghaddaszadeh-Ahrabi, Pourya Davoudi, Siavash Salek Ardestani, Natalia A. Zinovieva, Tatiana E. Deniskova and Anna M. Johansson

Genes 2021, 12(3), 433; https://doi.org/10.3390/genes12030433 - 17 Mar 2021

Cited by 3 | Viewed by 4175

Abstract

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt [...] Read more.

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation F_ST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the F_ST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep. Full article

(This article belongs to the Section Animal Genetics and Genomics)

► Show Figures

Figure 1

17 pages, 6332 KiB

Open AccessArticle

Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in Dendrobium Officinale

by Yaling Chen, Benchang Hu, Fantao Zhang, Xiangdong Luo and Jiankun Xie

Genes 2021, 12(3), 432; https://doi.org/10.3390/genes12030432 - 17 Mar 2021

Cited by 4 | Viewed by 2333

Abstract

Dendrobium officinale is a rare and traditional medicinal plant with high pharmacological and nutritional value. The self-incompatibility mechanism of D. officinale reproductive isolation was formed in the long-term evolution process, but intraspecific hybridization of different germplasm resources leads to a large gap in [...] Read more.

Dendrobium officinale is a rare and traditional medicinal plant with high pharmacological and nutritional value. The self-incompatibility mechanism of D. officinale reproductive isolation was formed in the long-term evolution process, but intraspecific hybridization of different germplasm resources leads to a large gap in the yield, quality, and medicinal value of D. officinale. To investigate the biological mechanism of self-incompatibility in D. officinale, cytological observation and the transcriptome analysis was carried out on the samples of self-pollination and cross-pollination in D. officinale. Results for self-pollination showed that the pollen tubes could grow in the style at 2 h, but most of pollen tubes stopped growing at 4 h, while a large number of cross-pollinated pollen tubes grew along the placental space to the base of ovary, indicating that the self-incompatibility of D. officinale may be gametophyte self-incompatibility. A total of 63.41 G basesum of D. officinale style samples from non-pollinated, self-pollination, and cross-pollination by RNA-seq were obtained, and a total of 1944, 1758, and 475 differentially expressed genes (DEGs) in the comparison of CK (non-pollinated) vs. HF (cross-pollination sample), CK vs. SF (self-pollination sample) and SF vs. HF were identified, respectively. Forty-one candidate genes related to self-incompatibility were found by function annotation of DEGs, including 6 Ca²⁺ signal genes, 4 armed repeat containing (ARC) related genes, 11 S-locus receptor kinase (SRK) related genes, 2 Exo70 family genes, 9 ubiquitin related genes, 1 fatty acid related gene, 6 amino acid-related genes, 1 pollen-specific leucine-rich repeat extensin-like protein (LRX) related gene and 1 lectin receptor-like kinases (RLKs) related gene, showed that self-incompatibility mechanism of D. officinale involves the interaction of multiple genes and pathways. The results can provide a basis for the study of the self-incompatibility mechanism of D. officinale, and provide ideas for the preservation and utilization of high-quality resources of D. officinale. Full article

(This article belongs to the Special Issue Genetic Research of Sex Determination)

► Show Figures

Figure 1

20 pages, 4354 KiB

Open AccessArticle

Phenotypical Characterization and Neurogenic Differentiation of Rabbit Adipose Tissue-Derived Mesenchymal Stem Cells

by Mária Tirpáková, Jaromír Vašíček, Andrea Svoradová, Andrej Baláži, Marián Tomka, Miroslav Bauer, Alexander Makarevich and Peter Chrenek

Genes 2021, 12(3), 431; https://doi.org/10.3390/genes12030431 - 17 Mar 2021

Cited by 10 | Viewed by 3105

Abstract

Although the rabbit is a frequently used biological model, the phenotype of rabbit adipose-derived mesenchymal stem cells (rAT-MSCs) is not well characterized. One of the reasons is the absence of specific anti-rabbit antibodies. The study aimed to characterize rAT-MSCs using flow cytometry and [...] Read more.

Although the rabbit is a frequently used biological model, the phenotype of rabbit adipose-derived mesenchymal stem cells (rAT-MSCs) is not well characterized. One of the reasons is the absence of specific anti-rabbit antibodies. The study aimed to characterize rAT-MSCs using flow cytometry and PCR methods, especially digital droplet PCR, which confirmed the expression of selected markers at the mRNA level. A combination of these methods validated the expression of MSCs markers (CD29, CD44, CD73, CD90 and CD105). In addition, cells were also positive for CD49f, vimentin, desmin, α-SMA, ALDH and also for the pluripotent markers: NANOG, OCT4 and SOX2. Moreover, the present study proved the ability of rAT-MSCs to differentiate into a neurogenic lineage based on the confirmed expression of neuronal markers ENO2 and MAP2. Obtained results suggest that rAT-MSCs have, despite the slight differences in marker expression, the similar phenotype as human AT-MSCs and possess the neurodifferentiation ability. Accordingly, rAT-MSCs should be subjected to further studies with potential application in veterinary medicine but also, in case of their cryopreservation, as a source of genetic information of endangered species stored in the gene bank. Full article

(This article belongs to the Special Issue Application Status and Development Prospects of Stem Cells)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Genes, Volume 12, Issue 3 (March 2021) – 139 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI