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Plant Phylogenomics and Genetic Diversity 2.0
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Plant Phylogenomics and Genetic Diversity 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 2435

Special Issue Editor

Dr. Wenpan Dong

E-Mail Website
Guest Editor
Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
Interests: chloroplast genome evolution; DNA barcoding; plant genetic diversity; plant phylogenomics; Oleaceae; medicinal plants; biogeography; molecular evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Phylogenomics is the intersection of the fields of phylogeny and genomics. Phylogenomics aims at reconstructing the evolutionary histories of organisms, taking into account whole genomes or large fractions of genomes. Compared with traditional phylogenetic studies, phylogenomics has the advantage of manipulating a large amount of information to produce more reliable results. The challenge is to make the best use of genomic data to establish robust and realistic phylogenetic relationships and elucidate evolutionary relationships. The genomic era has arrived, and more than 1000 plant genome sequences have been published, representing 788 different species. Genetic diversity serves as a way for populations to adapt to changing environments. The development of phylogenomics will bring new insights into the study of population genetics in terms of population structure, population history, geographic isolation, gene flow, ecological and genomic interactions, and genotype–phenotype relationships.

This Special Issue welcomes manuscripts that advance the knowledge and understanding of plant phylogeny, evolutionary history, and genetic diversity on a genomic basis. Topics covered by this Special Issue include, but are not limited to, the following:

  • Establishment and clarification of plant evolutionary relationships.
  • Gene family evolution.
  • Species diversity.
  • Improvements in methods for acquiring genomic data.
  • Plant speciation.
  • Ecological and genomic interactions.
  • Genotype–phenotype relationships.

Dr. Wenpan Dong
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 phylogenomics
  • genome
  • gene evolution
  • species diversity
  • speciation
  • ecogenomics

Related Special Issue

Published Papers (3 papers)

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Research

18 pages, 2621 KiB  
Article
Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome
by Valentina Rudenko and Eugene Korotkov
Int. J. Mol. Sci. 2024, 25(8), 4441; https://doi.org/10.3390/ijms25084441 - 18 Apr 2024
Viewed by 393
Abstract
In this study, we applied the iterative procedure (IP) method to search for families of highly diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains over 16 million bases. The algorithm included the construction of position weight matrices (PWMs) for [...] Read more.
In this study, we applied the iterative procedure (IP) method to search for families of highly diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains over 16 million bases. The algorithm included the construction of position weight matrices (PWMs) for repeat families and the identification of more dispersed repeats based on the PWMs using dynamic programming. The results showed that the C. merolae genome contained 20 repeat families comprising a total of 33,938 dispersed repeats, which is significantly more than has been previously found using other methods. The repeats varied in length from 108 to 600 bp (522.54 bp in average) and occupied more than 72% of the C. merolae genome, whereas previously identified repeats, including tandem repeats, have been shown to constitute only about 28%. The high genomic content of dispersed repeats and their location in the coding regions suggest a significant role in the regulation of the functional activity of the genome. Full article
(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity 2.0)
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19 pages, 6962 KiB  
Article
Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom
by Hanbing Cai, Rong Xu, Ping Tian, Mengjie Zhang, Ling Zhu, Tuo Yin, Hanyao Zhang and Xiaozhen Liu
Int. J. Mol. Sci. 2024, 25(1), 257; https://doi.org/10.3390/ijms25010257 - 23 Dec 2023
Cited by 1 | Viewed by 879
Abstract
Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and [...] Read more.
Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae. Full article
(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity 2.0)
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15 pages, 4812 KiB  
Article
Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots
by Cheng-Yuan Zhou, Wen-Jun Lin, Ruyi Li, Yuhan Wu, Zhong-Jian Liu and Ming-He Li
Int. J. Mol. Sci. 2024, 25(1), 184; https://doi.org/10.3390/ijms25010184 - 22 Dec 2023
Viewed by 676
Abstract
Angraecum, commonly known as Darwin’s orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of Angraecum were firstly reported and the [...] Read more.
Angraecum, commonly known as Darwin’s orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of Angraecum were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine–cytosine (GC) content of 36.6–36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all ndh genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (trnSGCU-trnGGCC, ycf1-trnNGGU, trnNGUU-rpl32, psaC-ndhE and trnSGCU-trnGGCC) and five protein-coding genes (rpl32, rps16, psbK, rps8, and ycf1) were identified. The consistent and robust phylogenetic relationships of Angraecum were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus Angraecum was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for Angraecum. Full article
(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity 2.0)
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