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Diversity
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Comparative and Functional Genomics of Land Plants
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Comparative and Functional Genomics of Land Plants

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (15 July 2022) | Viewed by 7278

Special Issue Editors

Dr. Chen Jiao

E-Mail Website1 Website2
Guest Editor
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
Interests: plant evolution; comparative genomics; population genetics; bioinformatics
Prof. Dr. Xuepeng Sun

E-Mail Website
Guest Editor
College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
Interests: bioinformatics; plant genomics; evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The biological system on the earth is, at its core, a flow of genetic information from the extinguished ancestors (source) to the extant species (branched targets), during which mutation, selection, gene flow and genetic drift act on to modify its elements and affect the translation to phenotypes. In plants, studying how gene and genome have evolved is critical for understanding the evolution of morphological and physiological diversities that is often in response to environmental shifts, and predicting prospective changes that plants may have in the face of new challenges.

With the increasing availability of plant genome sequences, much insight can be gleaned from comparative/population genomics approaches. This Special Issue focuses on plant evolutionary genomics and welcomes studies that use a combination of interdisciplinary approaches to understand key questions of plant evolution.

Dr. Chen Jiao
Dr. Xuepeng Sun
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. Diversity 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 evolution
  • Evolutionary genomics
  • Comparative genomics
  • Population genomics

Published Papers (3 papers)

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Research

16 pages, 3691 KiB  
Article
Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species
by Ting Ren, Xueyimu Aou, Rongming Tian, Zhenbing Li, Chang Peng and Xingjin He
Diversity 2022, 14(5), 323; https://doi.org/10.3390/d14050323 - 21 Apr 2022
Cited by 5 | Viewed by 2088
Abstract
Cnidium monnieri is an economically important traditional Chinese medicinal plant. In this study, the complete chloroplast (cp) genome of C. monnieri was determined using the Illumina paired-end sequencing, the GetOrganelle de novo assembly strategy, as well as the GeSeq annotation method. Our results [...] Read more.
Cnidium monnieri is an economically important traditional Chinese medicinal plant. In this study, the complete chloroplast (cp) genome of C. monnieri was determined using the Illumina paired-end sequencing, the GetOrganelle de novo assembly strategy, as well as the GeSeq annotation method. Our results showed that the cp genome was 147,371 bp in length with 37.4% GC content and included a large single-copy region (94,361 bp) and a small single-copy region (17,552 bp) separated by a pair of inverted repeat regions (17,729 bp). A total of 129 genes were contained in the cp genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also investigated codon usage, RNA editing, repeat sequences, simple sequence repeats (SSRs), IR boundaries, and pairwise Ka/Ks ratios. Four hypervariable regions (trnD-trnY-trnE-trnT, ycf2, ndhF-rpl32-trnL, and ycf1) were identified as candidate molecular markers for species authentication. The phylogenetic analyses supported non-monophyly of Cnidium and C. monnieri located in tribe Selineae based on the cp genome sequences and internal transcribed spacer (ITS) sequences. The incongruence of the phylogenetic position of C. monnieri between ITS and cpDNA phylogenies suggested that C. monnieri might have experienced complex evolutions with hybrid and incomplete lineage sorting. All in all, the results presented herein will provide plentiful chloroplast genomic resources for studies of the taxonomy, phylogeny, and species authentication of C. monnieri. Our study is also conducive to elucidating the phylogenetic relationships and taxonomic position of Cnidium. Full article
(This article belongs to the Special Issue Comparative and Functional Genomics of Land Plants)
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7 pages, 1287 KiB  
Article
A Proposal for the Lectotype Designation of Ishige foliacea (Phaeophyceae, Ishigeaceae) Using DNA Barcoding
by Eun-Young Lee, Soon Jeong Lee and Sang-Rae Lee
Diversity 2022, 14(3), 225; https://doi.org/10.3390/d14030225 - 19 Mar 2022
Cited by 1 | Viewed by 1736
Abstract
Three species of the genus Ishige (Phaeophyceae, Ishigeaceae) are known from Korea, Japan and Mexico; they include Ishige foliacea Okamura, I. okamurae Yendo and I. sinicola (Setchell and N.L. Gardner) Chihara. Two species, I. foliacea and I. okamurae, are present in the [...] Read more.
Three species of the genus Ishige (Phaeophyceae, Ishigeaceae) are known from Korea, Japan and Mexico; they include Ishige foliacea Okamura, I. okamurae Yendo and I. sinicola (Setchell and N.L. Gardner) Chihara. Two species, I. foliacea and I. okamurae, are present in the algal flora of Korea and Japan. The original description of I. okamurae defined two forms of branches, filiform and foliose, but later the foliose branch was recognized as a new species I. foliacea, which is epiphytic on I. okamurae but can also be free-living. The currently proposed lectotype for I. foliacea is based on a free-living form and does not reflect the intent of the original description of the species. In this study, we conducted the DNA barcoding for herbarium specimens to identify Ishige species. Additionally, the variation in cox3 sequences obtained from I. okamurae specimens with two morphological forms collected from waters around the Korean Peninsula was sufficient to separate two species, I. okamurae and its epiphyte I. foliacea. The epiphytic I. foliacea on the lectotype specimen of I. okamurae is designated as lectotype I. foliacea. Full article
(This article belongs to the Special Issue Comparative and Functional Genomics of Land Plants)
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14 pages, 37135 KiB  
Article
Distinct Reproductive Strategy of Two Endemic Amazonian Quillworts
by Cecilio F. Caldeira, Arthur V. S. Lopes, Keyvilla C. Aguiar, Aline L. Ferreira, João V. S. Araujo, Vinnícius M. S. Gomes, Daniel B. Zandonadi, Cinthia B. Abranches, Silvio J. Ramos, Markus Gastauer, Naiara V. Campos, Lísia M. S. Gestinari, Luis A. Prado, Fernando M. G. Santos, Rodrigo L. Martins, Francisco A. Esteves, Guilherme Oliveira and Mirella P. Santos
Diversity 2021, 13(8), 348; https://doi.org/10.3390/d13080348 - 29 Jul 2021
Cited by 7 | Viewed by 2855
Abstract
We examined the reproductive strategy of two Amazonian quillworts (Isoëtes cangae and Isoëtes serracarajensis), endemic and threatened species of canga ecosystems. Sexual propagation was examined by in vitro fertilization assays, while asexual propagation was examined by tiller emission. Isoëtes cangae is [...] Read more.
We examined the reproductive strategy of two Amazonian quillworts (Isoëtes cangae and Isoëtes serracarajensis), endemic and threatened species of canga ecosystems. Sexual propagation was examined by in vitro fertilization assays, while asexual propagation was examined by tiller emission. Isoëtes cangae is an outcrossing species that reproduces exclusively by spore germination and is able to propagate by self- and cross-fertilization. Isoëtes serracarajensis reproduces asexually by emitting tillers from the plant corm, despite producing male and female sporangia. These distinct reproductive strategies in the different species may be linked to their contrasting habitats. Isoëtes cangae inhabit a permanent oligotrophic lake with mild environmental changes, while I. serracarajensis are found in temporary ponds facing severe seasonal drought, where asexual propagation may represent an adaptive advantage to the short growth period during access to water. We also observed different relationships between plant growth and reproductive traits between the species, despite their common production of sporophytes with high survival rates. Together, these results are of paramount importance for establishing conservation plans for both species considering the advantages of sexual propagation to maintain the genetic diversity of I. cangae and the diligent management required to do the same with asexually propagated I. serracarajensis. Full article
(This article belongs to the Special Issue Comparative and Functional Genomics of Land Plants)
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