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Plant Plastid Genome and Phylogenetics
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Plant Plastid Genome and Phylogenetics

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

Deadline for manuscript submissions: closed (10 November 2024) | Viewed by 6454

Special Issue Editors

Dr. Guiqi Bi

E-Mail Website
Guest Editor
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
Interests: plant genetics
Dr. Min Cao

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Guest Editor
College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
Interests: algae genetic breeding; non-coding RNAs
Dr. Luodong Huang

E-Mail Website
Guest Editor
Department of Biological Sciences, College of Life Science and Technology, Guangxi University, Nanning 530004, China
Interests: plant genetics; organellar genomes; transcriptome regulation

Special Issue Information

Dear Colleagues,

We are pleased to announce the upcoming Special Issue of the journal Genes, and cordially invite you to contribute your valuable research in this field. This Special Issue aims to explore and discuss the latest advancements and breakthroughs in plant plastid genome research, with a specific focus on phylogenetics.

Plant plastid genomes play a crucial role in plant evolution, diversity and resource utilization. Exploring and understanding the plastid genome sequences provides valuable insights into plant phylogenetic relationships, population genetics and species conservation. In recent years, significant progress has been made in unraveling the complexities of plant plastid genomes and their applications in phylogenetics.

This Special Issue aims to bring together researchers from various disciplines to present their cutting-edge research in plant plastid genome studies and explore the implications of phylogenetic analysis. It will provide a platform for scientists to share their findings, methodologies and perspectives on plant genetics and genomics.

We welcome contributions that cover a broad range of topics, including, but not limited to:

  • Comparative plastid genomics;
  • Phylogenetic analysis using plastid genomes;
  • Evolutionary dynamics of plastid genomes;
  • Functional and structural aspects of plastid genomes;
  • Plastid genome engineering and applications;
  • Plastid genome evolution and adaptation.

We encourage the submission of original research articles, reviews and perspectives that delve into the various aspects of plant plastid genome and phylogenetics. We are particularly interested in studies that provide novel insights, innovative methodologies and significant contributions to the field. All submitted papers will undergo a rigorous peer-review process to ensure high quality and scientific integrity.

Dr. Guiqi Bi
Dr. Min Cao
Dr. Luodong Huang
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. 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 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 plastid genome
  • phylogenetics
  • comparative genomics
  • evolutionary biology

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Published Papers (4 papers)

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Research

11 pages, 1481 KiB  
Article
Analysis of Codon Usage Bias in Chloroplast Genomes of Dryas octopetala var. asiatica (Rosaceae)
by Lizhen Ling, Shudong Zhang and Tao Yang
Genes 2024, 15(7), 899; https://doi.org/10.3390/genes15070899 - 9 Jul 2024
Viewed by 888
Abstract
Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species [...] Read more.
Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species have not yet been documented. This study sequenced and assembled the complete genome of D. octopetala var. asiatica. The annotated genes in the chloroplast genome were analyzed for codon composition through multivariate statistical methods including a neutrality plot, a parity rule 2 (PR2) bias plot, and an effective number of codons (ENC) plot using CodonW 1.4.2 software. The results indicated that the mean GC content of 53 CDSs was 38.08%, with the average GC content at the third codon base position being 27.80%, suggesting a preference for A/U(T) at the third codon position in chloroplast genes. Additionally, the chloroplast genes exhibited a weak overall codon usage bias (CUB) based on ENC values and other indicators. Correlation analysis showed a significant negative correlation between ENC value and GC2, an extremely positive correlation with GC3, but no correlation with GC1 content. These findings highlight the importance of the codon composition at the third position in influencing codon usage bias. Furthermore, our analysis indicated that the CUB of the chloroplast genome of D. octopetala var. asiatica was primarily influenced by natural selection and other factors. Finally, this study identified UCA, CCU, GCU, AAU, GAU, and GGU as the optimal codons. These results offer a foundational understanding for genetic modification and evolutionary dynamics of the chloroplast genome of D. octopetala var. asiatica. Full article
(This article belongs to the Special Issue Plant Plastid Genome and Phylogenetics)
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12 pages, 3039 KiB  
Article
Complete Chloroplast Genome Sequence Structure and Phylogenetic Analysis of Kohlrabi (Brassica oleracea var. gongylodes L.)
by Mengliang Zhao, Yanxun Wu and Yanjing Ren
Genes 2024, 15(5), 550; https://doi.org/10.3390/genes15050550 - 26 Apr 2024
Cited by 1 | Viewed by 1110
Abstract
Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes [...] Read more.
Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes were identified, including 87 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The base composition analysis showed that the overall GC content was 36.36% of the complete chloroplast genome sequence. Relative synonymous codon usage frequency (RSCU) analysis showed that most codons with values greater than 1 ended with A or U, while most codons with values less than 1 ended with C or G. Thirty-five scattered repeats were identified and most of them were distributed in the large single-copy (LSC) region. A total of 290 simple sequence repeats (SSRs) were found and 188 of them were distributed in the LSC region. Phylogenetic relationship analysis showed that five Brassica oleracea subspecies were clustered into one group and the kohlrabi chloroplast genome was closely related to that of B. oleracea var. botrytis. Our results provide a basis for understanding chloroplast-dependent metabolic studies and provide new insight for understanding the polyploidization of Brassicaceae species. Full article
(This article belongs to the Special Issue Plant Plastid Genome and Phylogenetics)
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16 pages, 4644 KiB  
Article
First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae)
by Tae-Hee Kim, Young-Ho Ha, Hiroaki Setoguchi, Kyung Choi, Sang-Chul Kim and Hyuk-Jin Kim
Genes 2024, 15(3), 380; https://doi.org/10.3390/genes15030380 - 20 Mar 2024
Cited by 1 | Viewed by 1257
Abstract
Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes [...] Read more.
Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73–106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33–40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China. Full article
(This article belongs to the Special Issue Plant Plastid Genome and Phylogenetics)
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17 pages, 5469 KiB  
Article
Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of Capsicum pubescens Ruiz & Pav
by Di Wu, Wenting Fu, Gaoling Fan, Dongfu Huang, Kangyun Wu, Yongfa Zhan, Xiangmin Tu and Jianwen He
Genes 2024, 15(2), 152; https://doi.org/10.3390/genes15020152 - 24 Jan 2024
Cited by 1 | Viewed by 2180
Abstract
Chilean peppers, cultivated from Capsicum pubescens, are globally renowned as popular vegetable and spice crops. C. pubescens belongs to the Capsicum L. (pepper) family and is one of the five pepper cultivars grown in China. In this study, we assembled and annotated [...] Read more.
Chilean peppers, cultivated from Capsicum pubescens, are globally renowned as popular vegetable and spice crops. C. pubescens belongs to the Capsicum L. (pepper) family and is one of the five pepper cultivars grown in China. In this study, we assembled and annotated the complete mt genome of C. pubescens. We investigated several aspects of its genome, including characteristics, codon usage, RNA editing sites, repeat sequences, selective pressure, gene clusters, and phylogenetic relationships. Furthermore, we compared it with other plant mt genomes. The data we obtained will provide valuable information for studying evolutionary processes in the Capsicum genus and will assist in the functional analysis of Capsicum mitogenomes. Full article
(This article belongs to the Special Issue Plant Plastid Genome and Phylogenetics)
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