Molecular Phylogenetics and Phylogeography of Seed Plants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 September 2023) | Viewed by 5159

Special Issue Editor


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Guest Editor
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
Interests: population genomics; population genetics; comparative and evolutionary genomics; molecular evolution; speciation; phylogeography

Special Issue Information

Dear Colleagues,

With the rapid development of sequencing technology, the cost of acquiring genomic sequences has decreased dramatically. Consequently, large amounts of genomic data for seed plants have been generated in recent decades. Thus, we have encountered an excellent opportunity to conduct research at the genomic level on the phylogenetics and phylogeography of seed plants. Genome-scale phylogenetic analyses, or phylogenomics, can yield greater confidence of inferred phylogenic relationships with little systematic bias, which is usually difficult in analyses using one or several gene sequences. Unlike phylogenomics, it is still a challenge for phylogeographic researchers to use population NGS data due to the difficulty of inferring haplotypic data from short reads sequences. Fortunately, programs with specific algorithms, such as BEAGLE and SHAPEIT, have been developed and can be used to impute and accurately phase population genomic data. This Special Issue of Genes on the “Molecular Phylogenetics and Phylogeography of Seed Plants” will highlight how genomics technologies can be applied to improve research in this field. The Special Issue will provide an overview of recent developments in this field of research, including critical perspectives on current and upcoming challenges.

Dr. Fumin Zhang
Guest Editor

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Keywords

  • seed plant
  • phylogenomics
  • genome-scale phylogenetics
  • population genomics
  • population genetic structure
  • haplotype inferring
  • population demography

Published Papers (4 papers)

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Research

11 pages, 3010 KiB  
Article
Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica
by Meixia Wang, Lei Huang, Yixuan Kou, Danqi Li, Wan Hu, Dengmei Fan, Shanmei Cheng, Yi Yang and Zhiyong Zhang
Genes 2023, 14(10), 1971; https://doi.org/10.3390/genes14101971 - 21 Oct 2023
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Abstract
Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes [...] Read more.
Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world’s most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Phylogeography of Seed Plants)
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19 pages, 1200 KiB  
Article
Insights into the Adaptation to High Altitudes from Transcriptome Profiling: A Case Study of an Endangered Species, Kingdonia uniflora
by Man-Li Nong, Xiao-Hui Luo, Li-Xin Zhu, Ya-Nan Zhang, Xue-Yi Dun and Lei Huang
Genes 2023, 14(6), 1291; https://doi.org/10.3390/genes14061291 - 19 Jun 2023
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Abstract
Kingdonia uniflora is an endangered alpine herb that is distributed along an altitudinal gradient. The unique traits and important phylogenetic position make K. uniflora an ideal model for exploring how endangered plants react to altitude variation. In this study, we sampled nine individuals [...] Read more.
Kingdonia uniflora is an endangered alpine herb that is distributed along an altitudinal gradient. The unique traits and important phylogenetic position make K. uniflora an ideal model for exploring how endangered plants react to altitude variation. In this study, we sampled nine individuals from three representative locations and adopted RNA-seq technology to sequence 18 tissues, aiming to uncover how K. uniflora responded to different altitudes at the gene expression level. We revealed that genes that responded to light stimuli and circadian rhythm genes were significantly enriched in DEGs in the leaf tissue group, while genes that were related to root development and peroxidase activity or involved in the pathways of cutin, suberin, wax biosynthesis, and monoterpenoid biosynthesis were significantly enriched in DEGs in the flower bud tissue group. All of the above genes may play an important role in the response of K. uniflora to various stresses, such as low temperatures and hypoxia in high-altitude environments. Furthermore, we proved that the discrepancy in gene expression patterns between leaf and flower bud tissues varied along the altitudinal gradient. Overall, our findings provide new insights into the adaptation of endangered species to high-altitude environments and further encourage parallel research to focus on the molecular mechanisms of alpine plant evolution. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Phylogeography of Seed Plants)
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10 pages, 2767 KiB  
Article
Genetic Diversity and Population Differentiation of a Chinese Endangered Plant Ammopiptanthus nanus (M. Pop.) Cheng f.
by Aoran Li, Miao Ma, Haotian Li, Songfeng He and Shugao Wang
Genes 2023, 14(5), 1020; https://doi.org/10.3390/genes14051020 - 29 Apr 2023
Cited by 2 | Viewed by 1508
Abstract
Ammopiptanthus nanus (M. Pop.) Cheng f. is a very important resource plant that integrates soil and water conservation, afforestation of barren mountains, and ornamental, medicinal, and scientific research functions and is also a critically endangered plant in China, remaining in only six small [...] Read more.
Ammopiptanthus nanus (M. Pop.) Cheng f. is a very important resource plant that integrates soil and water conservation, afforestation of barren mountains, and ornamental, medicinal, and scientific research functions and is also a critically endangered plant in China, remaining in only six small fragmented populations in the wild. These populations have been suffering from severe anthropomorphic disturbances, causing further losses in genetic diversity. However, its genetic diversity level and genetic differentiation degree among the fragmented populations are still unclear. Inthis study, DNA was extracted from fresh leaves from the remnant populations of A. nanus, and the inter-simple-sequence repeat (ISSR) molecular marker system was used to assess its level of genetic diversity and differentiation. The result was that its genetic diversity is low at both species and population levels, with only 51.70% and 26.84% polymorphic loci, respectively. The Akeqi population had the highest genetic diversity, whereas the Ohsalur and Xiaoerbulak populations had the lowest. There was significant genetic differentiation among the populations, and the value of the genetic differentiation coefficient (Gst) was as high as 0.73, while the gene flow value was as low as 0.19 owing to spatial fragmentation and a serious genetic exchange barrier among the populations. It is suggested that a nature reserve and germplasm banks should be established as soon as possible for elimination of the anthropomorphic disturbances, and mutual introductions between the populations and introduced patches of the species, such as with habitat corridors or stepping stones, should be performed simultaneously to improve the genetic diversity of the isolated populations for the conservation of this plant. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Phylogeography of Seed Plants)
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22 pages, 3003 KiB  
Article
A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of Populus davidiana
by Dandan Zhao, Jianguo Zhang, Nan Hui, Li Wang, Yang Tian, Wanning Ni, Jinhua Long, Li Jiang, Yi Li, Songfeng Diao, Jinhua Li, Luke R. Tembrock, Zhiqiang Wu and Zhaoshan Wang
Genes 2023, 14(4), 821; https://doi.org/10.3390/genes14040821 - 29 Mar 2023
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Abstract
Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate [...] Read more.
Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan–Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai–Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Phylogeography of Seed Plants)
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