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Advances in Evolution of Plant Organelle Genome (Volume II)
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Advances in Evolution of Plant Organelle Genome (Volume II)

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

Deadline for manuscript submissions: 10 October 2024 | Viewed by 5568

Special Issue Editor

Prof. Dr. Zhiqiang Wu

E-Mail Website
Guest Editor
Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Interests: organelle genome; chloroplast; mitochondria; phylogeny; population genomics; RNA editing; transfer; pan-organelle genome; organelle mutation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the development of genome sequencing, an increasing amount of genome data from thousands of species have been decoded. The analysis of organelle genomes also provides suitable opportunities. However, chloroplast and mitochondria in plants are faced with different research circumstances. What kind of evolutionary forces are shaping their destiny? How large is the scale of their variations? How can we decode the variations between these two organelle genomes? What are their connections with the nuclear genome? These and many other burning questions mean that an in-depth exploration of their properties is urgently needed.

According to the endosymbiont hypothesis, organelles originated billions of years ago. Nevertheless, the changes that organelles have undergone in that time have been indiscernible, and it is thus incredibly hard to distinguish the differences between contemporary organelles and their ancestral bacteria. How can we then explore and understand those changes using genomic methods and data?

In this Special Issue, we aim to focus on the evolution of the plant organelle genome, including chloroplast and mitochondria. Our goal is to include research on organelle genome variations, transfer between organelle genomes, and organelle genome mutations, all of which will help us to develop a deeper understanding of the plant organelle genome.

Studies including genomic dry data and experimental wet lab data on the organelle genome are all welcome. Research on morphological characters, evolutionary variations within and among populations, functional variations, connections among organelle genomes, and other related topics is invited.

If you are interested in contributing to this Special Issue, please let us know as soon as possible. We look forward to receiving your contributions.

Prof. Dr. Zhiqiang Wu
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 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

  • organelle genome
  • chloroplast
  • mitochondria
  • phylogeny
  • population genomics
  • RNA editing
  • transfer
  • pan-organelle genome

Published Papers (7 papers)

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Research

15 pages, 3700 KiB  
Article
Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis
by Peng Wei, Youzheng Li, Mei Ke, Yurong Hou, Abudureyimu Aikebaier and Zinian Wu
Genes 2024, 15(5), 546; https://doi.org/10.3390/genes15050546 (registering DOI) - 25 Apr 2024
Viewed by 221
Abstract
Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we [...] Read more.
Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of K. ewersmanniana and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of K. ewersmanniana reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in K. ewersmanniana, with some genes (rps19, ndhF, ycf1) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed Krascheninnikovia ceratoides, Dysphania ambrosioides, Dysphania pumilio, and Dysphania botrys to have a close monophyletic relationship. By sequencing the K. ewersmanniana chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome (Volume II))
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14 pages, 4422 KiB  
Article
Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective
by Sijia Zhang, Shiyun Han, De Bi, Jianke Yang, Wen Ge, Yuanxin Ye, Jinming Gao, Chenwei Dai and Xianzhao Kan
Genes 2024, 15(4), 444; https://doi.org/10.3390/genes15040444 - 31 Mar 2024
Viewed by 601
Abstract
Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies [...] Read more.
Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome (Volume II))
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14 pages, 6013 KiB  
Article
Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics
by Junhu Kan, Shuo Zhang, Zhiqiang Wu and De Bi
Genes 2024, 15(4), 441; https://doi.org/10.3390/genes15040441 - 30 Mar 2024
Viewed by 542
Abstract
The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are [...] Read more.
The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome (Volume II))
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11 pages, 6732 KiB  
Article
High-Quality Assembly and Analysis of the Complete Mitogenomes of German Chamomile (Matricaria recutita) and Roman Chamomile (Chamaemelum nobile)
by Jun Yang, Xinting Zhang, Zixuan Hua, Hongna Jia, Keke Li and Chengcheng Ling
Genes 2024, 15(3), 301; https://doi.org/10.3390/genes15030301 - 26 Feb 2024
Viewed by 696
Abstract
German chamomile (Matricaria chamomilla L.) and Roman chamomile (Chamaemelum nobile) are the two well-known chamomile species from the Asteraceae family. Owing to their essential oils and higher medicinal value, these have been cultivated widely across Europe, Northwest Asia, North America, [...] Read more.
German chamomile (Matricaria chamomilla L.) and Roman chamomile (Chamaemelum nobile) are the two well-known chamomile species from the Asteraceae family. Owing to their essential oils and higher medicinal value, these have been cultivated widely across Europe, Northwest Asia, North America, and Africa. Regarding medicinal applications, German chamomile is the most commonly utilized variety and is frequently recognized as the “star among medicinal species”. The insufficient availability of genomic resources may negatively impact the progression of chamomile industrialization. Chamomile’s mitochondrial genome is lacking in extensive empirical research. In this study, we achieved the successful sequencing and assembly of the complete mitochondrial genome of M. chamomilla and C. nobile for the first time. An analysis was conducted on codon usage, sequence repeats within the mitochondrial genome of M. chamomilla and C. nobile. The phylogenetic analysis revealed a consistent positioning of M. chamomilla and C. nobile branches within both mitochondrial and plastid-sequence-based phylogenetic trees. Furthermore, the phylogenetic analysis also showed a close relationship between M. chamomilla and C. nobile within the clade comprising species from the Asteraceae family. The results of our analyses provide valuable resources for evolutionary research and molecular barcoding in chamomile. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome (Volume II))
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15 pages, 2734 KiB  
Article
The Complete Mitochondrial Genome of Paeonia lactiflora Pall. (Saxifragales: Paeoniaceae): Evidence of Gene Transfer from Chloroplast to Mitochondrial Genome
by Pan Tang, Yang Ni, Jingling Li, Qianqi Lu, Chang Liu and Jinlin Guo
Genes 2024, 15(2), 239; https://doi.org/10.3390/genes15020239 - 14 Feb 2024
Viewed by 1134
Abstract
Paeonia lactiflora (P. lactiflora), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate [...] Read more.
Paeonia lactiflora (P. lactiflora), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate this matter, we sequenced and characterized the mitochondrial genome (mitogenome) of P. lactiflora. Similar to the chloroplast genome (cpgenome), the mitogenome of P. lactiflora extends across 181,688 base pairs (bp). Its unique quadripartite structure results from a pair of extensive inverted repeats, each measuring 25,680 bp in length. The annotated mitogenome includes 27 protein-coding genes, 37 tRNAs, 8 rRNAs, and two pseudogenes (rpl5, rpl16). Phylogenetic analysis was performed to identify phylogenetic trees consistent with Paeonia species phylogeny in the APG Ⅳ system. Moreover, a total of 12 MTPT events were identified and 32 RNA editing sites were detected during mitogenome analysis of P. lactiflora. Our research successfully compiled and annotated the mitogenome of P. lactiflora. The study provides valuable insights regarding the taxonomic classification and molecular evolution within the Paeoniaceae family. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome (Volume II))
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15 pages, 7569 KiB  
Article
Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation
by Liang Ma, Cheng-Yuan Zhou, Jin-Liao Chen, Ding-Kun Liu, Siren Lan and Zhong-Jian Liu
Genes 2024, 15(1), 20; https://doi.org/10.3390/genes15010020 - 22 Dec 2023
Viewed by 850
Abstract
Luisia, a genus of the subtribe Aeridinae of Orchidaceae, comprises ca. 40 species. Members of Luisia exhibit unique morphological characteristics and represent a valuable ornamental orchid genus. However, due to the scarcity of distinct morphological characters, species identification within this genus is [...] Read more.
Luisia, a genus of the subtribe Aeridinae of Orchidaceae, comprises ca. 40 species. Members of Luisia exhibit unique morphological characteristics and represent a valuable ornamental orchid genus. However, due to the scarcity of distinct morphological characters, species identification within this genus is ambiguous and controversial. In the present study, next-generation sequencing (NGS) methods were used to assemble the plastomes of five Luisia species and compare them with one publicly available Luisia plastid genome data. The plastomes of Luisia possessed a quadripartite structure, with sizes ranging from 146,243 bp to 147,430 bp. The plastomes of six Luisia species contained a total of 120 genes, comprising 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. Notably, all ndh genes were pseudogenized or lost. An analysis of codon usage bias showed that leucine (Leu) exhibited the highest frequency, while cysteine (Cys) exhibited the lowest frequency. A total of 57 to 64 SSRs and 42 to 49 long repeats were identified. Five regions and five coding sequences were identified for DNA barcodes, based on the nucleotide diversity (Pi) analysis. The species of Luisia constituted a monophyletic group and were sister to Paraphalaenopsis with strong support. Our study deepens the understanding of species identification, plastome evolution and the phylogenetic positions of Luisia. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome (Volume II))
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14 pages, 9641 KiB  
Article
Comparative Plastomes of Curcuma alismatifolia (Zingiberaceae) Reveal Diversified Patterns among 56 Different Cut-Flower Cultivars
by Jie Wang, Xuezhu Liao, Yongyao Li, Yuanjun Ye, Guoming Xing, Shenglong Kan, Liyun Nie, Sen Li, Luke R. Tembrock and Zhiqiang Wu
Genes 2023, 14(9), 1743; https://doi.org/10.3390/genes14091743 - 31 Aug 2023
Cited by 1 | Viewed by 921
Abstract
Curcuma alismatifolia (Zingiberaceae) is an ornamental species with high economic value due to its recent rise in popularity among floriculturists. Cultivars within this species have mixed genetic backgrounds from multiple hybridization events and can be difficult to distinguish via morphological and histological methods [...] Read more.
Curcuma alismatifolia (Zingiberaceae) is an ornamental species with high economic value due to its recent rise in popularity among floriculturists. Cultivars within this species have mixed genetic backgrounds from multiple hybridization events and can be difficult to distinguish via morphological and histological methods alone. Given the need to improve identification resources, we carried out the first systematic study using plastomic data wherein genomic evolution and phylogenetic relationships from 56 accessions of C. alismatifolia were analyzed. The newly assembled plastomes were highly conserved and ranged from 162,139 bp to 164,111 bp, including 79 genes that code for proteins, 30 tRNA genes, and 4 rRNA genes. The A/T motif was the most common of SSRs in the assembled genomes. The Ka/Ks values of most genes were less than 1, and only two genes had Ka/Ks values above 1, which were rps15 (1.15), and ndhl (1.13) with petA equal to 1. The sequence divergence between different varieties of C. alismatifolia was large, and the percentage of variation in coding regions was lower than that in the non-coding regions. Such data will improve cultivar identification, marker assisted breeding, and preservation of germplasm resources. Full article
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome (Volume II))
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