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Tropical and Subtropical Plant Genomics
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Tropical and Subtropical Plant Genomics

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: closed (31 March 2023) | Viewed by 3026

Special Issue Editor

Prof. Dr. Lizhi Gao

E-Mail Website
Guest Editor
Asia-Pacific Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China
Interests: comparative genomics; population genomics; ecological genomics; conservation genomics; bioinformatics

Special Issue Information

Dear Colleagues,

Recent decades have witnessed rapid advances in genome sequencing technologies and a great development in bioinformatics tools towards bigdata mining of increasingly huge genomic information. The quick growths of genomics have unprecedentedly improved our knowledge about plant ecology, evolution, conservation, development, breeding and germplasm utilization. This special Issue aims to report the recent progress obtained in genomics studies in tropical and subtropical plants. It includes, but is not limited to, genome sequencing and assembly, genome structure and organization, comparative genomics, pan-genome analyses, population genomics, evolutionary genomics, ecological genomics, conservation genomics, gene family evolution, gene editing, RNA sequencing, the functions of specific genes, protein–protein interaction, biosynthesis pathways, epigenomics, SNP discovery, genome-wide association studies, and genomic selection. The bioinformatics tools and genome databases are also welcome.

Prof. Dr. Lizhi Gao
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.

Published Papers (2 papers)

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Research

20 pages, 8394 KiB  
Article
Comparative Genomic Analysis of Asian Cultivated Rice and Its Wild Progenitor (Oryza rufipogon) Has Revealed Evolutionary Innovation of the Pentatricopeptide Repeat Gene Family through Gene Duplication
by Li-Ying Feng, Pei-Fan Lin, Rong-Jing Xu, Hai-Qi Kang and Li-Zhi Gao
Int. J. Mol. Sci. 2023, 24(22), 16313; https://doi.org/10.3390/ijms242216313 - 14 Nov 2023
Cited by 1 | Viewed by 931
Abstract
The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the [...] Read more.
The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the PPR gene family in O. sativa and its wild progenitor, O. rufipogon, and outlined a comprehensive landscape of gene duplications. Our findings suggest that the majority of PPR genes originated from dispersed duplications. Although segmental duplications have only expanded approximately 11.30% and 13.57% of the PPR gene families in the O. sativa and O. rufipogon genomes, we interestingly obtained evidence that segmental duplication promotes the structural diversity of PPR genes through incomplete gene duplications. In the O. sativa and O. rufipogon genomes, 10 (~33.33%) and 22 pairs of gene duplications (~45.83%) had non-PPR paralogous genes through incomplete gene duplication. Segmental duplications leading to incomplete gene duplications might result in the acquisition of domains, thus promoting functional innovation and structural diversification of PPR genes. This study offers a unique perspective on the evolution of PPR gene structures and underscores the potential role of segmental duplications in PPR gene structural diversity. Full article
(This article belongs to the Special Issue Tropical and Subtropical Plant Genomics)
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24 pages, 10626 KiB  
Article
The Complete Chloroplast Genomes of Nine Smilacaceae Species from Hong Kong: Inferring Infra- and Inter-Familial Phylogeny
by Kwan-Ho Wong, Tin-Yan Siu, Stacey Shun-Kei Tsang, Bobby Lim-Ho Kong, Hoi-Yan Wu, Grace Wing-Chiu But, Jerome Ho-Lam Hui, Pang-Chui Shaw and David Tai-Wai Lau
Int. J. Mol. Sci. 2023, 24(8), 7460; https://doi.org/10.3390/ijms24087460 - 18 Apr 2023
Cited by 2 | Viewed by 1669
Abstract
The Smilacaceae is a cosmopolitan family consisting of 200–370 described species. The family includes two widely accepted genera, namely Smilax and Heterosmilax. Among them, the taxonomical status of Heterosmilax has been continuously challenged. Seven Smilax and two Heterosmilax species can be found [...] Read more.
The Smilacaceae is a cosmopolitan family consisting of 200–370 described species. The family includes two widely accepted genera, namely Smilax and Heterosmilax. Among them, the taxonomical status of Heterosmilax has been continuously challenged. Seven Smilax and two Heterosmilax species can be found in Hong Kong, with most of them having medicinal importance. This study aims to revisit the infra-familial and inter-familial relationships of the Smilacaceae using complete chloroplast genomes. The chloroplast genomes of the nine Smilacaceae species from Hong Kong were assembled and annotated, which had sizes of 157,885 bp to 159,007 bp; each of them was identically annotated for 132 genes, including 86 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. The generic status of Heterosmilax was not supported because it was nested within the Smilax clade in the phylogenetic trees, echoing previous molecular and morphological studies. We suggest delimitating the genus Heterosmilax as a section under the genus Smilax. The results of phylogenomic analysis support the monophyly of Smilacaceae and the exclusion of Ripogonum from the family. This study contributes to the systematics and taxonomy of monocotyledons, authentication of medicinal Smilacaceae, and conservation of plant diversity. Full article
(This article belongs to the Special Issue Tropical and Subtropical Plant Genomics)
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