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

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. Genes 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 2400 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.

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

Title: Phylogenetics of rice based on genome-wide expression data
Authors: Meixia Wang
Affiliation: Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China

Title: Phylogenetics of pinus based on chloroplast genome
Authors: Yixuan Kou
Affiliation: Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China

Title: Phylogeny and chloroplast genome evolution of Gesneriaceae
Authors: Liang Tang
Affiliation: Center for Terrestrial Biodiversity of the South China Sea, Hainan University

Title: Comparative transcriptomics reveals selection patterns during pea domestication
Authors: Rong Liu
Affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Title: Population genetics researchof Miscanthus nudipes and M. nepalensis
Authors: Ma Hongzheng
Affiliation: Tianjin Agricultural University

Title: The phylogeny of the BEP clade in grasses and systematic position of the tribe Stipeae: Evidence from the whole-genome SNP data
Authors: Xieyong Zhang
Affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China

Title: Insights on the adaptation to high altitude from transcriptome profiling：A case study of an endangered species Kingdonia uniflora
Authors: Man-Li Nong; Xiao-Hui Luo; Li-Xin Zhu; Ya-Nan Zhang; Xue-Yi Dun; Lei Huang
Affiliation: College of Life Sciences, Shaanxi Normal University
Abstract: Kingdonia uniflora is an alpine endangered herb which distributed along altitudinal gradient. The unique traits and important phylogenetic position make K. uniflora an ideal model for exploring how endangered plants react to the altitude variation. In this study, we sampled 9 individuals from three representative locations and adopted RNA-seq technology to sequence 18 tissues, aiming to uncover how K. uniflora responded to different altitude on gene expression level. We revealed that genes responded to light stimulus and circadian rhythm genes were significantly enriched DEGs in leaf tissue group, while genes that were related to root development and peroxidase activity, or involved with pathway of cutin, suberin, wax biosynthesis and monoterpenoid biosynthesis were significantly enriched DEGs in flower bud tissue group. All of the above genes might play an important role in the response of K. uniflora to various stresses like low temperature, hypoxia in high altitude environment. Furthermore, we proved that the discrepancy of gene expression pattern between leaf and flower bud tissue varied along altitudinal gradient. Overall, our findings provided new insights into the adaptation of endangered species to high altitude environment and would encourage more parallel researches to focus on the molecular mechanism of alpine plants’ evolution.

Title: Mining plant height QTL using Bulk Segregant Analysis Sequencing based on NGS in Yuanjiang Oryza rufipogon
Authors: Xiaoming Zheng
Affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China