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Investigate the Genome and Functional Variation/Mechanism of Plant Organelles on Individual and Population Levels

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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 (30 November 2023) | Viewed by 12962

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Dr. Zhiqiang Wu

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Shenzhen Branch, 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: plant organelle; organelle genome variation; organelle genome mutation; organelle genome recombination; pan-organelle genome; method to assemble the organelle genome
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Special Issue Information

Dear Colleagues,

Plants contain two organelles, including the mitochondrion and the chloroplast, retaining their own genomes that have originated independently from nuclear genomes and are thought to be residual genomes from ancient eubacteria. Those two organelles play an essential role in plant cell energy and other important metabolism, crossing the whole plant life. With the fast development of sequencing technologies and decreasing the cost, the complete genomes from thousands of species have been decoded in recent decades. Those independent organelle genomes have also been finished at the same time; however, they are in an uneven state for mitochondrion and chloroplast. How to fill the gap between those organelles is still a challenge caused by the complex structural variations. What kinds of different evolutionary forces are underlying those? Additionally, how can we decode those variations? How large a scale of the variations exist among the diversified plant species? There are so many interesting questions that are waiting to be studied deeply.

In this specific Organelle Research Special Issue, we want to call for papers on the evolutionary and functional variation of plant organelle genome, including the chloroplast and mitochondria. The topic can extend into the method of organelle genome assemblies (including the methods about annotation, visualization, structural variation); genome variations (on gene function, RNA editing, horizontal gene transfer, and organelle databases); genome applications (on organelle-based phylogenetics, population genomics, and pan-organelle genome); and genome editing on organelle genome. Reviews on each research point of the above are also invited, and about the computational methods are also encouraged. Studies including the genomic dry data and experimental wet lab data on organelle genome are all welcomed. Since IJMS is a journal of molecular science, thus pure bioinformatics analysis will not be suitable for our journal. You can add some molecular experiments to it.

If you are interested in contributing, please let us know as soon as possible. We are looking forward to your reply and certainly hope for appositive answer.

Dr. Zhiqiang Wu
Guest Editor

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Keywords

organelle genome
organelle databases
organelle genome phylogeny
organelle population genomics
organelle RNA editing
pan-organelle genome
cyto-nuclear interactions
organelle methodologies
organelle genome assembly, visualization and structural variation

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Research

19 pages, 8031 KiB

Open AccessArticle

Assembly of the Complete Mitochondrial Genome of Pereskia aculeata Revealed That Two Pairs of Repetitive Elements Mediated the Recombination of the Genome

by Xue Zhang, Yuanyu Shan, Jingling Li, Qiulin Qin, Jie Yu and Hongping Deng

Int. J. Mol. Sci. 2023, 24(9), 8366; https://doi.org/10.3390/ijms24098366 - 6 May 2023

Cited by 14 | Viewed by 2592

Abstract

Pereskia aculeata is a potential new crop species that has both food and medicinal (antinociceptive activity) properties. However, comprehensive genomic research on P. aculeata is still lacking, particularly concerning its organelle genome. In this study, P. aculeata was studied to sequence the mitochondrial genome (mitogenome) and to ascertain the assembly, informational content, and developmental expression of the mitogenome. The findings revealed that the mitogenome of P. aculeata is circular and measures 515,187 bp in length with a GC content of 44.05%. It contains 52 unique genes, including 33 protein-coding genes, 19 tRNA genes, and three rRNA genes. Additionally, the mitogenome analysis identified 165 SSRs, primarily consisting of tetra-nucleotides, and 421 pairs of dispersed repeats with lengths greater than or equal to 30, which were mainly forward repeats. Based on long reads and PCR experiments, we confirmed that two pairs of long-fragment repetitive elements were highly involved with the mitogenome recombination process. Furthermore, there were 38 homologous fragments detected between the mitogenome and chloroplast genome, and the longest fragment was 3962 bp. This is the first report on the mitogenome in the family Cactaceae. The decoding of the mitogenome of P. aculeata will provide important genetic materials for phylogenetic studies of Cactaceae and promote the utilization of species germplasm resources. Full article

(This article belongs to the Special Issue Investigate the Genome and Functional Variation/Mechanism of Plant Organelles on Individual and Population Levels)

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13 pages, 2819 KiB

Open AccessArticle

Comparative Analysis of Chloroplast Genome of Desmodium stryacifolium with Closely Related Legume Genome from the Phaseoloid Clade

by Le-Thi Yen, Muniba Kousar and Joonho Park

Int. J. Mol. Sci. 2023, 24(7), 6072; https://doi.org/10.3390/ijms24076072 - 23 Mar 2023

Cited by 9 | Viewed by 1820

Abstract

Desmodium styracifolium is a medicinal plant from the Desmodieae tribe, also known as Grona styracifolia. Its role in the treatment of urolithiasis, urinary infections, and cholelithiasis has previously been widely documented. The complete chloroplast genome sequence of D. Styracifolium is 149,155 bp in length with a GC content of 35.2%. It is composed of a large single copy (LSC) of 82,476 bp and a small single copy (SSC) of 18,439 bp, which are separated by a pair of inverted repeats (IR) of 24,120 bp each and has 128 genes. We performed a comparative analysis of the D. styracifolium cpDNA with the genome of previously investigated members of the Sesamoidea tribe and on the outgroup from its Phaseolinae sister tribe. The size of all seven cpDNAs ranged from 148,814 bp to 151,217 bp in length due to the contraction and expansion of the IR/SC boundaries. The gene orientation of the SSC region in D. styracifolium was inverted in comparison with the other six studied species. Furthermore, the sequence divergence of the IR regions was significantly lower than that of the LSC and the SSC, and five highly divergent regions, trnL-UAA-trnT-UGU, psaJ-ycf4, psbE-petL, rpl36-rps8, and rpl32-trnL-UGA, were identified that could be used as valuable molecular markers in future taxonomic studies and phylogenetic constructions. Full article

(This article belongs to the Special Issue Investigate the Genome and Functional Variation/Mechanism of Plant Organelles on Individual and Population Levels)

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16 pages, 3313 KiB

Open AccessArticle

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

by Rui-Sen Lu, Ke Hu, Feng-Jiao Zhang, Xiao-Qin Sun, Min Chen and Yan-Mei Zhang

Int. J. Mol. Sci. 2023, 24(4), 3341; https://doi.org/10.3390/ijms24043341 - 7 Feb 2023

Cited by 8 | Viewed by 2540

Abstract

Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I–IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC–petN, trnL–rpl32, ndhD–ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species. Full article

(This article belongs to the Special Issue Investigate the Genome and Functional Variation/Mechanism of Plant Organelles on Individual and Population Levels)

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21 pages, 6332 KiB

Open AccessArticle

A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms

by Kai-Yuan Huang, Sheng-Long Kan, Ting-Ting Shen, Pin Gong, Yuan-Yuan Feng, Hong Du, Yun-Peng Zhao, Tao Wan, Xiao-Quan Wang and Jin-Hua Ran

Int. J. Mol. Sci. 2022, 23(18), 10844; https://doi.org/10.3390/ijms231810844 - 16 Sep 2022

Cited by 3 | Viewed by 2163

Abstract

Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms. Full article

(This article belongs to the Special Issue Investigate the Genome and Functional Variation/Mechanism of Plant Organelles on Individual and Population Levels)

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19 pages, 3282 KiB

Open AccessArticle

Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications

by Shiyun Han, Rongbin Wang, Xin Hong, Cuilian Wu, Sijia Zhang and Xianzhao Kan

Int. J. Mol. Sci. 2022, 23(17), 10151; https://doi.org/10.3390/ijms231710151 - 5 Sep 2022

Cited by 12 | Viewed by 2466

Abstract

The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae. Full article

(This article belongs to the Special Issue Investigate the Genome and Functional Variation/Mechanism of Plant Organelles on Individual and Population Levels)

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