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Life
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Research Advances in Plant Genomics: 2nd Edition
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Research Advances in Plant Genomics: 2nd Edition

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: closed (24 November 2023) | Viewed by 11774

Special Issue Editors

Dr. Jitendra Kumar

E-Mail Website
Guest Editor
Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
Interests: plant pathology; molecular biology; functional genomics; reverse genetics
Special Issues, Collections and Topics in MDPI journals
Dr. Krishan Rai

E-Mail Website
Guest Editor
Plant Geneticist Lead, CoverCress Inc., Saint Louis, MO 63132, USA
Interests: plant molecular biology; genomics; gene editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The first volume of this Special Issue was a great success; therefore, we invite you to publish your research in the second volume of this Special Issue (https://www.mdpi.com/journal/life/special_issues/advances_plant_genomics).

The ever-increasing world population and shrinking farmland, coupled with abiotic and biotic stresses, threaten food insecurity for millions of people worldwide. Crop yield can be improved by increasing the number of grains produced per plant, the number of plants per unit area, and the size of grains. Plants genomics has demonstrated interesting insights into the mechanisms associated with growth, development, and stress responses, and can be exploited for the achievement of the aforementioned traits through genetic changes.

The aim of this research topic is to collect recent advances emphasizing the role of genomics in the selection and improvement of crop traits to meet the food requirements of the future. This Special Issue of “Plant Genomics” welcomes submissions of original research, review, or perspective articles addressing the current technical advances in plant genomics aimed at connecting plant physiological processes with gene expression dynamics during the growth and development of plants, flowering and grain filling, and abiotic as well as biotic stresses. Manuscripts highlighting the use of comparative genome analysis, transcriptomics, small RNAs, and other novel noncoding RNAs in plant research, in addition to those describing future challenges, are also welcome. Manuscripts utilizing advanced bioinformatics tools and databases for the purpose of enhancing the capabilities of existing plant genomics approaches for a better understanding of plant development are also encouraged for submission.

Dr. Jitendra Kumar
Dr. Krishan Rai
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant molecular biology
  • stress tolerance
  • disease resistance
  • trait improvement
  • genomics
  • transcriptomics
  • genome editing

Published Papers (5 papers)

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Research

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23 pages, 9990 KiB  
Article
De Novo Hybrid Assembled Draft Genome of Commiphora wightii (Arnott) Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis
by Rudra Prasad Banerjee, Gopal Ji Tiwari, Babita Joshi, Satya Narayan Jena, Om Prakash Sidhu, Baleshwar Meena, Tikam S. Rana and Saroj K. Barik
Life 2023, 13(3), 662; https://doi.org/10.3390/life13030662 - 28 Feb 2023
Cited by 2 | Viewed by 1804
Abstract
Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which [...] Read more.
Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine–cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics: 2nd Edition)
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18 pages, 2582 KiB  
Article
Characterization of Peroxidase and Laccase Gene Families and In Silico Identification of Potential Genes Involved in Upstream Steps of Lignan Formation in Sesame
by Yedomon Ange Bovys Zoclanclounon, Michael Rostás, Nam-Jin Chung, Youngjun Mo, Petr Karlovsky and Komivi Dossa
Life 2022, 12(8), 1200; https://doi.org/10.3390/life12081200 - 08 Aug 2022
Cited by 5 | Viewed by 2645
Abstract
Peroxidases and laccases are oxidative enzymes involved in physiological processes in plants, covering responses to biotic and abiotic stress as well as biosynthesis of health-promoting specialized metabolites. Although they are thought to be involved in the biosynthesis of (+)-pinoresinol, a comprehensive investigation of [...] Read more.
Peroxidases and laccases are oxidative enzymes involved in physiological processes in plants, covering responses to biotic and abiotic stress as well as biosynthesis of health-promoting specialized metabolites. Although they are thought to be involved in the biosynthesis of (+)-pinoresinol, a comprehensive investigation of this class of enzymes has not yet been conducted in the emerging oil crop sesame and no information is available regarding the potential (+)-pinoresinol synthase genes in this crop. In the present study, we conducted a pan-genome-wide identification of peroxidase and laccase genes coupled with transcriptome profiling of diverse sesame varieties. A total of 83 and 48 genes have been identified as coding for sesame peroxidase and laccase genes, respectively. Based on their protein domain and Arabidopsis thaliana genes used as baits, the genes were classified into nine and seven groups of peroxidase and laccase genes, respectively. The expression of the genes was evaluated using dynamic transcriptome sequencing data from six sesame varieties, including one elite cultivar, white vs black seed varieties, and high vs low oil content varieties. Two peroxidase genes (SiPOD52 and SiPOD63) and two laccase genes (SiLAC1 and SiLAC39), well conserved within the sesame pan-genome and exhibiting consistent expression patterns within sesame varieties matching the kinetic of (+)-pinoresinol accumulation in seeds, were identified as potential (+)-pinoresinol synthase genes. Cis-acting elements of the candidate genes revealed their potential involvement in development, hormonal signaling, and response to light and other abiotic triggers. Transcription factor enrichment analysis of promoter regions showed the predominance of MYB binding sequences. The findings from this study pave the way for lignans-oriented engineering of sesame with wide potential applications in food, health and medicinal domains. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics: 2nd Edition)
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19 pages, 4993 KiB  
Article
Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat (Triticum aestivum L.)
by Shumayla, Venugopal Mendu, Kashmir Singh and Santosh Kumar Upadhyay
Life 2022, 12(7), 941; https://doi.org/10.3390/life12070941 - 23 Jun 2022
Cited by 11 | Viewed by 1985
Abstract
Proline-rich extensin-like receptor protein kinases (PERKs) are known for their roles in the developmental processes and stress responses of many plants. We have identified 30 TaPERK genes in the genome of T. aestivum, exploring their evolutionary and syntenic relationship and analyzing their [...] Read more.
Proline-rich extensin-like receptor protein kinases (PERKs) are known for their roles in the developmental processes and stress responses of many plants. We have identified 30 TaPERK genes in the genome of T. aestivum, exploring their evolutionary and syntenic relationship and analyzing their gene and protein structures, various cis-regulatory elements, expression profiling, and interacting miRNAs. The TaPERK genes formed 12 homeologous groups and clustered into four phylogenetic clades. All the proteins exhibited a typical domain organization of PERK and consisted of conserved proline residue repeats and serine-proline and proline-serine repeats. Further, the tyrosine-x-tyrosine (YXY) motif was also found conserved in thirteen TaPERKs. The cis-regulatory elements and expression profiling under tissue developmental stages suggested their role in plant growth processes. Further, the differential expression of certain TaPERK genes under biotic and abiotic stress conditions suggested their involvement in defense responses as well. The interaction of TaPERK genes with different miRNAs further strengthened evidence for their diverse biological roles. In this study, a comprehensive analysis of obtained TaPERK genes was performed, enriching our knowledge of TaPERK genes and providing a foundation for further possible functional analyses in future studies. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics: 2nd Edition)
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23 pages, 12686 KiB  
Article
Chloroplast Genome of Lithocarpus dealbatus (Hook.f. & Thomson ex Miq.) Rehder Establishes Monophyletic Origin of the Species and Reveals Mutational Hotspots with Taxon Delimitation Potential
by Rahul Gunvantrao Shelke, Rudra Prasad Banerjee, Babita Joshi, Prem Prakash Singh, Gopal Ji Tiwari, Dibyendu Adhikari, Satya Narayan Jena and Saroj Kanta Barik
Life 2022, 12(6), 828; https://doi.org/10.3390/life12060828 - 02 Jun 2022
Cited by 2 | Viewed by 1861
Abstract
There is phylogenetic ambiguity in the genus Lithocarpus and subfamily Quercoideae (Family: Fagaceae). Lithocarpus dealbatus, an ecologically important tree, is the dominant species among the Quercoideae in India. Although several studies have been conducted on the species’ regeneration and ecological and economic [...] Read more.
There is phylogenetic ambiguity in the genus Lithocarpus and subfamily Quercoideae (Family: Fagaceae). Lithocarpus dealbatus, an ecologically important tree, is the dominant species among the Quercoideae in India. Although several studies have been conducted on the species’ regeneration and ecological and economic significance, limited information is available on its phylo-genomics. To resolve the phylogeny in Quercoideae, we sequenced and assembled the 161,476 bp chloroplast genome of L. dealbatus, which has a large single-copy section of 90,732 bp and a small single-copy region of 18,987 bp, separated by a pair of inverted repeat regions of 25,879 bp. The chloroplast genome contained 133 genes, of which 86 were protein-coding genes, 39 were transfer RNAs, and eight were ribosomal RNAs. Analysis of repeat elements and RNA editing sites revealed interspecific similarities within the Lithocarpus genus. DNA diversity analysis identified five highly diverged coding and noncoding hotspot regions in the four genera, which can be used as polymorphic markers for species/taxon delimitation across the four genera of Quercoideae viz., Lithocarpus, Quercus, Castanea, and Castanopsis. The chloroplast-based phylogenetic analysis among the Quercoideae established a monophyletic origin of Lithocarpus, and a closer evolutionary lineage with a few Quercus species. Besides providing insights into the chloroplast genome architecture of L. dealbatus, the study identified five mutational hotspots having high taxon-delimitation potential across four genera of Quercoideae. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics: 2nd Edition)
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Review

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13 pages, 1309 KiB  
Review
Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review
by Vincent Pamugas Reyes, Justine Kipruto Kitony, Shunsaku Nishiuchi, Daigo Makihara and Kazuyuki Doi
Life 2022, 12(11), 1752; https://doi.org/10.3390/life12111752 - 01 Nov 2022
Cited by 10 | Viewed by 2588
Abstract
Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development [...] Read more.
Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development of different genotyping techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled the parallel sequencing and genotyping of hundreds of samples in a single run, making it more cost-effective. Currently, GBS is being used in several pre-breeding programs of rice to identify beneficial genes and QTL from different rice genetic resources. In this review, we present the current advances in the utilization of genotyping-by-sequencing for the development of rice pre-breeding materials and the improvement of existing rice cultivars. The challenges and perspectives of using this approach are also highlighted. Full article
(This article belongs to the Special Issue Research Advances in Plant Genomics: 2nd Edition)
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