Plant Chloroplast Genome and Evolution

Topic Information

Dear Colleagues,

The chloroplast plays a crucial role in the energy metabolism of plant cells. Its genomes are an essential part of data for phylogenetic and evolutionary studies. With the development of genome sequencing technology, plastid genomes from thousands of plant species have been deciphered, which provides suitable opportunities for organelle genome analysis. Plastid genomes have also been used to reconstruct deep phylogenetic relationships, to derive reticulate evolutionary histories or to phylogenetically place taxa. Despite the upsurge in popularity, decades of studies have raised controversy on the advantages and shortcomings of plastome phylogenomics. Features such as the inheritance characteristics of plastomes, recombination, gene transfer, or specific evolutionary patterns may result in wrong inferences. Whereas tree discordances often are the primary indication for such problems, the underlying mechanisms need to be more extensively explored. The challenges and possible workarounds for such issues with plastome data have to be addressed clearly, and it is essential to show which situations plastome phylogenomics can contribute to, and to find explanations for situations where they fail to do so. Meanwhile, recognition or accreditation standards for plastid genomic applications remain limited, and there is a need for an effective standardisation of methods for generating, analysing and conducting organelle genomic experiments. In this Topic, we hope to collect new plant plastid genomes and to infer phylogenetic correlations. Our aims are to investigate plastid genome features, transfer between organelle genomes and organelle genome mutations, with a focus on their morphological characteristics, evolutionary variation within and between populations, functional variation, and other relevant research topics. All of these will help us to deepen our understanding of plant plastid genomes. If you are interested in contributing to this topic, please let us know as soon as possible. We look forward to hearing from you.

Prof. Dr. Chao Shi
Dr. Lassaâd Belbahri
Dr. Shuo Wang
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Diversity diversity	2.1	3.4	2009	15.4 Days	CHF 2100	Submit
Forests forests	2.4	4.4	2010	16.9 Days	CHF 2600	Submit
Genes genes	2.8	5.2	2010	16.3 Days	CHF 2600	Submit
International Journal of Plant Biology ijpb	-	2.0	2010	19.2 Days	CHF 1200	Submit
Plants plants	4.0	6.5	2012	18.2 Days	CHF 2700	Submit

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Published Papers (10 papers)

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Open AccessArticle

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

by Yunqing Gao, Zhenjiang Chen, Xiuzhang Li, Kamran Malik and Chunjie Li

Genes 2024, 15(2), 226; https://doi.org/10.3390/genes15020226 - 10 Feb 2024

Cited by 1 | Viewed by 1110

Abstract

The present study provides a detailed analysis of the chloroplast genome of Microula sikkimensis. The genome consisted of a total of 149,428 bp and four distinct regions, including a large single-copy region (81,329 bp), a small single-copy region (17,261 bp), and an [...] Read more.

The present study provides a detailed analysis of the chloroplast genome of Microula sikkimensis. The genome consisted of a total of 149,428 bp and four distinct regions, including a large single-copy region (81,329 bp), a small single-copy region (17,261 bp), and an inverted repeat region (25,419 bp). The genome contained 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, and some exhibited duplication in the inverted repeat region. The chloroplast genome displayed different GC content across regions, with the inverted repeat region exhibiting the highest. Codon usage analysis and the identification of simple sequence repeats (SSRs) offer valuable genetic markers. Comparative analysis with other Boraginaceae species highlighted conservation and diversity in coding and noncoding regions. Phylogenetic analysis placed M. sikkimensis within the Boraginaceae family, revealing its distinct relationship with specific species. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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15 pages, 6247 KiB  

Open AccessArticle

Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny

by Jie Huang, Zhaocen Lu, Chunrui Lin, Weibin Xu and Yan Liu

Genes 2023, 14(10), 1894; https://doi.org/10.3390/genes14101894 - 29 Sep 2023

Cited by 2 | Viewed by 2773

Abstract

Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species [...] Read more.

Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species are mainly based on their specialized and diverse floral structures. Aspidistra plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of Aspidistra. In this study, we reported chloroplast (cp) genomes of seven Aspidistra species (A. crassifila, A. dolichanthera, A. erecta, A. longgangensis, A. minutiflora, A. nankunshanensis, and A. retusa). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of Aspidistra cp genomes. We identified eight divergent hotspot regions (trnC-GCA-petN, trnE-UUC-psbD, accD-psaI, petA-psbJ, rpl20-rps12, rpl36-rps8, ccsA-ndhD and rps15-ycf1) that serve as potential molecular markers. Our newly generated Aspidistra plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of Aspidistra species. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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16 pages, 4183 KiB  

Open AccessArticle

Genetic Diversity and Structure of Geodorum eulophioides, a Plant Species with Extremely Small Populations in China

by Zhi Li, Zhaohui Ran, Yang Zhang, Xu Xiao and Mingtai An

Diversity 2023, 15(9), 990; https://doi.org/10.3390/d15090990 - 3 Sep 2023

Viewed by 1104

Abstract

Geodorum eulophioides is a unique and endangered species belonging to the Orchidaceae family in China. It has great potential as an ornamental horticultural plant. However, little is known about its genetic diversity and reasons for being endangered due to its narrow distribution and [...] Read more.

Geodorum eulophioides is a unique and endangered species belonging to the Orchidaceae family in China. It has great potential as an ornamental horticultural plant. However, little is known about its genetic diversity and reasons for being endangered due to its narrow distribution and few populations in the wild. To effectively evaluate and conserve available resources, the genetic diversity and population structure of G. eulophioides were analyzed in this study. A total of 94 individuals from 10 natural populations were studied using site-specific amplified fragment sequencing (SLAF-seq). Based on the 76,340 SNPs detected by SLAF-seq, genetic diversity analysis was performed and markers associated with environmental variables were determined. The results showed that the level of genetic diversity in the 10 natural populations studied was low, with PIC values ranging from 0.1874 to 0.2156. FIS values ranged from −0.2376 to 0.2658, with excess and deficiency in heterozygotes. FST values ranged from 0.0482 to 0.3144, with genetic variation among populations. AMOVA results showed that the genetic variation among populations accounted for 21.35% of the total variation, and the remaining genetic variation among individuals within populations was 78.65%. The results of the population structure analysis showed that 94 individuals were classified into three major groups and two subgroups. Environmental association analysis using Bayenv2 and LFMM yielded thirty and eighteen putative adaptive loci, respectively, and five specific functional genes were annotated. In summary, this study provides further insight into the genetic structure of G. eulophioides and provides a reference for protection and restoration. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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14 pages, 4943 KiB  

Open AccessArticle

Pueraria montana Population Structure and Genetic Diversity Based on Chloroplast Genome Data

by Jiahui Sun, Yiheng Wang, Ping Qiao, Lei Zhang, Enze Li, Wenpan Dong, Yuping Zhao and Luqi Huang

Plants 2023, 12(12), 2231; https://doi.org/10.3390/plants12122231 - 6 Jun 2023

Cited by 5 | Viewed by 1750

Abstract

Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To mine Pueraria montana chloroplast genome variation architecture and phylogeny, we investigated the chloroplast variation architecture of 104 P. montana accessions from across China. [...] Read more.

Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To mine Pueraria montana chloroplast genome variation architecture and phylogeny, we investigated the chloroplast variation architecture of 104 P. montana accessions from across China. P. montana’s chloroplast genome showed high diversity levels, with 1674 variations, including 1118 single nucleotide polymorphisms and 556 indels. The intergenic spacers, psbZ-trnS and ccsA-ndhD, are the two mutation hotspot regions in the P. montana chloroplast genome. Phylogenetic analysis based on the chloroplast genome dataset supported four P. montana clades. P. montana variations were conserved among and within clades, which showed high gene flow levels. Most P. montana clades were estimated to have diverged at 3.82–5.17 million years ago. Moreover, the East Asian summer monsoon and South Asian summer monsoon may have accelerated population divergence. Our results show that chloroplast genome sequences were highly variable and can be used as molecular markers to assess genetic variation and relationships in P. montana. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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18 pages, 3843 KiB  

Open AccessArticle

Complete Chloroplast Genome Determination of Ranunculus sceleratus from Republic of Korea (Ranunculaceae) and Comparative Chloroplast Genomes of the Members of the Ranunculus Genus

by Kang-Rae Kim, So Young Park, Heesoo Kim, Jeong Min Hong, Sun-Yu Kim and Jeong-Nam Yu

Genes 2023, 14(6), 1149; https://doi.org/10.3390/genes14061149 - 25 May 2023

Cited by 3 | Viewed by 1764

Abstract

Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed [...] Read more.

Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE, ndhF, rpl23, atpF, rps4, and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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15 pages, 7229 KiB  

Open AccessArticle

Complete Chloroplast Genome of Bamboo Species Pleioblastus ovatoauritus and Comparative Analysis of Pleioblastus from China and Japan

by Weihan Peng, Beibei Wang, Zhuolong Shen and Qirong Guo

Forests 2023, 14(5), 1051; https://doi.org/10.3390/f14051051 - 19 May 2023

Viewed by 2276

Abstract

Pleioblastus ovatoauritus T.H.Wen ex W.Y.Zhang is bamboo species published in 2018, originated from and existing in southeastern China. The chloroplast genome of Pl. ovatoauritus was obtained using a high-throughput sequencing platform. The chloroplast genome is up to 139,708 bp in length and displays [...] Read more.

Pleioblastus ovatoauritus T.H.Wen ex W.Y.Zhang is bamboo species published in 2018, originated from and existing in southeastern China. The chloroplast genome of Pl. ovatoauritus was obtained using a high-throughput sequencing platform. The chloroplast genome is up to 139,708 bp in length and displays a typical quadripartite structure with one large single-copy region, one small single-copy region, and two inverted repeat regions. There are 82 protein-coding genes, 8 rRNA genes, and 39 tRNA genes in the plastome genome. However, the interspecific relationship of Pleioblastus species originated from China and Japan has not been revealed explicitly. To understand their relationship, data from four Chinese species and four Japanese species were selected to investigate the distinctions between their genome structures, codon usage patterns, and SSR sites. We moved forward to examine the sequence divergence and polymorphic sites between the eight species. Phylogenetic trees were then plotted using the maximum likelihood method based on different parts of the sequences. Obvious difference found in the JLB boundary and a split in the phylograms contributed to our decision to split Pleioblastus species of China and Japan into different clades. Moreover, taxonomy using the subgenera concept in Flora Reipublicae Popularis Sinicae proved untenable. Nine SSR primers for Pleioblastus genus were then developed from cp genomes, aimed at facilitating identification and germplasm investigation. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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21 pages, 1439 KiB  

Open AccessArticle

Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China

by Jing Chen, Kaibing Zhou and Xinwen Hu

Genes 2023, 14(5), 1083; https://doi.org/10.3390/genes14051083 - 14 May 2023

Cited by 1 | Viewed by 1513

Abstract

The differences in cpDNA SNPs and InDels of 13 samples from single trees of different species or populations of oil-tea camellia in South China were examined in this study, and phylogenetic trees were reconstructed based on CDSs and non-CDSs of cpDNAs to research [...] Read more.

The differences in cpDNA SNPs and InDels of 13 samples from single trees of different species or populations of oil-tea camellia in South China were examined in this study, and phylogenetic trees were reconstructed based on CDSs and non-CDSs of cpDNAs to research the evolutionary relationships among all samples. The SNPs of all samples included all kinds of substitutions, and the frequency of the transition from AT to GC was highest; meanwhile, the frequencies of all kinds of transversions differed among the samples, and the SNPs exhibited polymorphism. The SNPs were distributed in all the different functional regions of cpDNAs, and approximately half of all SNPs in exons led to missense mutations and the gain or loss of termination codons. There were no InDels in the exons of any cpDNA samples, except those retrieved from Camellia gigantocarpa, although this InDel did not lead to a frame shift. The InDels of all cpDNA samples were unevenly distributed in the intergenic region and upstream and downstream of genes. The genes, regions of the same gene, sites and mutation types in the same region related to the distributions of SNPs, and InDels were inconsistent among samples. The 13 samples were divided into 2 clades and 7 or 6 subclades, and the samples of species from the same sections of the Camellia genus did not belong to the same subclades. Meanwhile, the genetic relationship between the samples of Camellia vietnamensis and the undetermined species from Hainan Province or the population of C. gauchowensis in Xuwen was closer than that between C. vietnamensis and the population of C. gauchowensis in Luchuan, and the genetic relationship among C. osmantha, C. vietnamensis and C. gauchowensis was very close. In sum, SNPs and InDels in the different cpDNAs resulted in variable phenotypes among the different species or populations, and they could be developed into molecular markers for studies on species and population identification and phylogenetic relationships. The conclusion from the identification of undetermined species from Hainan Province and the phylogenetic relationships among 13 oil-tea camellia samples based on cpCDS and cpnon-CDS sequences were the same as those from the former report. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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13 pages, 9477 KiB  

Open AccessArticle

Characterization of the Plastid Genome of the Vulnerable Endemic Indosasa lipoensis and Phylogenetic Analysis

by Ming-Li Wu, Rong-Rong Yan, Xue Xu, Guang-Qian Gou and Zhao-Xia Dai

Diversity 2023, 15(2), 197; https://doi.org/10.3390/d15020197 - 1 Feb 2023

Cited by 2 | Viewed by 1857

Abstract

Indosasa lipoensis, an ornamental garden plant, belongs to the Indosasa genus of the subfamily Bambooaceae within Poaceae. Indosasa lipoensis is endangered and requires protection owing to its relatively narrow distribution area. Chloroplast (cp) genome offers a novel awareness of the evolutionary and [...] Read more.

Indosasa lipoensis, an ornamental garden plant, belongs to the Indosasa genus of the subfamily Bambooaceae within Poaceae. Indosasa lipoensis is endangered and requires protection owing to its relatively narrow distribution area. Chloroplast (cp) genome offers a novel awareness of the evolutionary and genetic variation of higher plants. Herein, we assembled and elucidated the complete cp genome of I. lipoensis, and compared it with four previously published cp genomes from this genus. The I. lipoensis cp genome was 139,655 bp in size, with a typical quadripartite structure, encompassing a large single-copy region (LSC, 83,256 bp), a small single-copy region (SSC, 12,809 bp), and a pair of inverted repeat regions (IR, 21,795 bp). The cp genome consisted of 130 genes with 84 protein-coding genes (CDS), 38 tRNA genes, and 8 rRNA genes. The plastomes were highly conservative, compared to other bamboo species, and exhibited similar patterns of codon usage, number of repeat sequences, and expansion and contraction of the IR boundary. Five hypervariable hotspots were identified as potential DNA barcodes, namely rbcL, petA, petB, trnL-UAG, and ndhE-ndhI, respectively. Phylogenetic analysis based on the complete cp genomes revealed, with high resolution, that I. lipoensis and I. gigantea were most closely related. Overall, these results provided valuable characterization for the future conservation, genetic evaluation, and the breeding of I. lipoensis. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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16 pages, 2484 KiB  

Open AccessArticle

Identification of Commercial Cultivars in the Tabebuia Alliance Using Genotyping-by-Sequencing

by Jngxiang Meng, Yong Zhang, Yongcheng Wei, Rongrong Li, Zhen Li and Chonglu Zhong

Forests 2023, 14(2), 271; https://doi.org/10.3390/f14020271 - 31 Jan 2023

Cited by 1 | Viewed by 1367

Abstract

The Tabebuia alliance is widely planted in tropical and subtropical countries. However, the lack of accurate taxonomic information for many commercial cultivars leads to commercial disputes. We sought to clarify the background of commercial cultivars in China and to provide a robust basis [...] Read more.

The Tabebuia alliance is widely planted in tropical and subtropical countries. However, the lack of accurate taxonomic information for many commercial cultivars leads to commercial disputes. We sought to clarify the background of commercial cultivars in China and to provide a robust basis for patent protection. We collected 82 Tabebuia cultivars and 12 reference individuals, then developed large-scale single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing. We obtained 73,219 SNPs from the test samples, which represented a substantial increase compared with previous studies of Tabebuia species. Based on these SNPs and a clustering analysis, we detected six species among the samples, as well as an uncertain population which may be a hybrid between Handroanthus impetiginosus (Mart. ex DC) Mattos and H. heptaphyllus (Vell.) Mattos. An analysis of genetic diversity to assess germplasm resources indicated that excessive heterozygosity of these cultivars in China, which may explain the genetic basis of “novel-preferred” selection in ornamental plants or a narrow genetic background. After rigorous selection, we identified numerous high-quality molecular markers for cultivar identification, then constructed a concise fingerprint with 54 SNPs. Our work clarifies the background information of commercial cultivars of Tabebuia in China and provides information for cultivar identification. It will serve as an important technical resource for genetic studies, and it will help to protect patents that involve Tabebuia species. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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16 pages, 2613 KiB  

Open AccessArticle

Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?—A Case Study of Pulsatilla patens (L.) Mill

by Kamil Szandar, Sawicki Jakub, Łukasz Paukszto, Katarzyna Krawczyk and Monika Szczecińska

Genes 2023, 14(1), 67; https://doi.org/10.3390/genes14010067 - 25 Dec 2022

Viewed by 1965

Abstract

Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the [...] Read more.

Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD—ccsA, rps4—rps16, and trnL(UAG)—ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes—11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset. Full article

(This article belongs to the Topic Plant Chloroplast Genome and Evolution)

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