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Lubna, Asaf S, Khan I, Jan R, Asif S, Bilal S, Kim KM, Al-Harrasi A. Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome. Sci Rep 2024; 14:14509. [PMID: 38914674 DOI: 10.1038/s41598-024-65073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa's plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.
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Affiliation(s)
- Lubna
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Ibrahim Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
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Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ping J, Hao J, Wang T, Su Y. Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae. FRONTIERS IN PLANT SCIENCE 2024; 15:1351388. [PMID: 38693922 PMCID: PMC11061511 DOI: 10.3389/fpls.2024.1351388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetics, comparative genomics, evolutionary biology, and genetic engineering. Nonetheless, research progress on plastid genomics in the Annonaceae has been relatively slow. In this study, we analyzed the structure and repetitive sequence features of plastomes from 28 Annonaceae species. Among them, Mitrephora tomentosa and Desmos chinensis were newly sequenced, with sizes of 160,157 bp and 192,167 bp, and GC contents of 38.3% and 38.4%, respectively. The plastome size in the Annonaceae ranged from 158,837 bp to 202,703 bp, with inverted repeat (IR) region sizes ranging from 64,621 bp to 25,861 bp. Species exhibiting expansion in the IR region showed an increase in plastome size and gene number, frequent boundary changes, different expansion modes (bidirectional or unidirectional), and an increase in repetitive sequences. Specifically, a large number of dispersed repetitive sequences lead to an increase in the size of the LSC region in Goniothalamus tamirensis. Phylogenetic analysis revealed Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. This research uncovers the structural variation characteristics of plastomes in the Annonaceae, providing valuable information for understanding the phylogeny and plastome evolution of Annonaceae.
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Affiliation(s)
- Jingyao Ping
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jing Hao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Research Institute of Sun Yat-Sen University, Shenzhen, China
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Chen LQ, Li X, Yao X, Li DZ, Barrett C, dePamphilis CW, Yu WB. Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae. PLANT MOLECULAR BIOLOGY 2024; 114:40. [PMID: 38622367 DOI: 10.1007/s11103-024-01440-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
Abstract
Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic Cuscuta have been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variations and reduction of plastome has not been well investigated. In this study, we assembled and collected 40 plastid genomes belonging to 23 species representing four subgenera of Cuscuta and ten species of autotrophic Convolvulaceae. Our findings revealed nine types of structural variations and six types of inverted repeat (IR) boundary variations in the plastome of Convolvulaceae spp. These structural variations were associated with the shift of parasitic lifestyle, and IR boundary shift, as well as the abundance of long repeats. Overall, the degradation of Cuscuta plastome proceeded gradually, with one clade exhibiting an accelerated degradation rate. We observed five stages of gene loss in Cuscuta, including NAD(P)H complex → PEP complex → Photosynthesis-related → Ribosomal protein subunits → ATP synthase complex. Based on our results, we speculated that the shift of parasitic lifestyle in early divergent time promoted relaxed selection on plastomes, leading to the accumulation of microvariations, which ultimately resulted in the plastome reduction. This study provides new evidence towards a better understanding of plastomic evolution, variation, and reduction in the genus Cuscuta.
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Affiliation(s)
- Li-Qiong Chen
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Xin Li
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Division of BiologicalScience, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Xin Yao
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, State College, Pennsylvania, 16802, USA
| | - Wen-Bin Yu
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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Kan J, Zhang S, Wu Z, Bi D. Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics. Genes (Basel) 2024; 15:441. [PMID: 38674377 PMCID: PMC11049882 DOI: 10.3390/genes15040441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
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 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.
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Affiliation(s)
- Junhu Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
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Jost M, Wanke S. A comparative analysis of plastome evolution in autotrophic Piperales. AMERICAN JOURNAL OF BOTANY 2024; 111:e16300. [PMID: 38469876 DOI: 10.1002/ajb2.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
PREMISE Many plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed. METHODS We performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics. RESULTS We identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single-copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single-copy (LSC) region. CONCLUSIONS This study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR-LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene-like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR-SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high-quality plastomes based on de novo assembly methods and appropriate references for gene annotation.
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Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Botanik und Molekulare Evolutionsforschung, Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Biodiversität, Goethe-Universität, Frankfurt am Main, Germany
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Ha YH, Chang KS, Gil HY. Characteristics of chloroplast and mitochondrial genomes and intracellular gene transfer in the Korean endemic shrub, Sophora koreensis Nakai (Fabaceae). Gene 2024; 894:147963. [PMID: 37926173 DOI: 10.1016/j.gene.2023.147963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea
| | - Kae Sun Chang
- DMZ Botanic Garden, Korea National Arboretum, Yanggu-gun, Gangwon-do 24564, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea.
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Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
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Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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Kim SC, Ha YH, Park BK, Jang JE, Kang ES, Kim YS, Kimspe TH, Kim HJ. Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. PLoS One 2023; 18:e0289625. [PMID: 37733832 PMCID: PMC10513226 DOI: 10.1371/journal.pone.0289625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/24/2023] [Indexed: 09/23/2023] Open
Abstract
Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.
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Affiliation(s)
- Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Beom Kyun Park
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Ju Eun Jang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Eun Su Kang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Soo Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Tae-Hee Kimspe
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyuk-Jin Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
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Mu Z, Zhang Y, Zhang B, Cheng Y, Shang F, Wang H. Intraspecific Chloroplast Genome Variation and Domestication Origins of Major Cultivars of Styphnolobium japonicum. Genes (Basel) 2023; 14:1156. [PMID: 37372336 DOI: 10.3390/genes14061156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Styphnolobium japonicum is a significant resource of ornamental and medicinal plants. In this study, we employed high-throughput sequencing to assemble nine chloroplast genomes of S. japonicum. We compared and reconstructed the phylogenetic relationships of these genomes, along with three publicly available chloroplast genomes. Our results showed that the length of the 12 S. japonicum chloroplast genomes ranged from 158,613 bp to 158,837 bp, all containing 129 unique functional genes. The genetic diversity within S. japonicum chloroplast genomes was relatively low, with π = 0.00029, Theta-W = 0.00028, and an indel frequency of 0.62 indels/1 kb. Among the four regions, the SSC region exhibited the highest genetic diversity and indel frequency, while the IR region had the lowest. Non-coding regions displayed greater genetic variation compared to coding regions, with a few highly variable regions identified. The phylogenetic tree constructed revealed that the major cultivars of S. japonicum originated from two genetic 'sources. S. japonicum 'JinhuaiJ2' had an independent origin and showed close relatedness to S. japonicum var. violacea, S. japonicum var. japonicum, and S. japonicum f. oligophylla. On the other hand, other major cultivars shared a common genetic origin and were closely related to S. japonicum f. pendula. This study highlights the variability of chloroplast genomes within S. japonicum and provides insights into the genetic origins of major cultivars and their relationships with different varieties and forma.
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Affiliation(s)
- Zhiqiang Mu
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yu Zhang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Bin Zhang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yueqin Cheng
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Fude Shang
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongwei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
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11
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Wang Y, Zhang CF, Ochieng Odago W, Jiang H, Yang JX, Hu GW, Wang QF. Evolution of 101 Apocynaceae plastomes and phylogenetic implications. Mol Phylogenet Evol 2023; 180:107688. [PMID: 36581140 DOI: 10.1016/j.ympev.2022.107688] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/21/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Apocynaceae are one of the ten species-richest angiosperm families. However, the backbone phylogeny of the family is yet less well supported, and the evolution of plastome structure has not been thoroughly studied for the whole family. Herein, a total of 101 complete plastomes including 35 newly sequenced, 24 reassembled from public raw data and the rest from the NCBI GenBank database, representing 26 of 27 tribes of Apocynaceae, were used for comparative plastome analysis. Phylogenetic analyses were conducted using a combined plastid data matrix of 77 protein-coding genes from 162 taxa, encompassing all tribes and 41 of 49 subtribes of Apocynaceae. Plastome lengths ranged from 150,897 bp in Apocynum venetum to 178,616 bp in Hoya exilis. Six types of boundaries between the inverted repeat (IR) regions and single copy (SC) regions were identified. Different sizes of IR expansion were found in three lineages, including Alyxieae, Ceropegieae and Marsdenieae, suggesting multiple expansion events of the IRs over the SC regions in Apocynaceae. The IR regions of Marsdenieae evolved in two ways: expansion towards the large single copy (LSC) region in Lygisma + Stephanotis + Ruehssia + Gymnema (Cosmopolitan clade), and expansion towards both LSC and small single copy (SSC) region in Dischidia-Hoya alliance and Marsdenia (Asia-Pacific clade). Six coding genes and five non-coding regions were identified as highly variable, including accD, ccsA-ndhD, clpP, matK, ndhF, ndhG-ndhI, trnG(GCC)-trnfM(CAU), trnH(GUG)-psbA, trnY(GUA)-trnE(UUC), ycf1, and ycf2. Maximum likelihood and Bayesian phylogenetic analyses resulted in nearly identical tree topologies and produced a well-resolved backbone comprising 15 consecutive dichotomies that subdivided Apocynaceae into 15 clades. The subfamily Periplocoideae were embedded in the Apocynoid grade and were sister to the Echiteae-Odontadenieae-Mesechiteae clade with high support values. Three tribes (Melodineae, Vinceae, and Willughbeieae), the subtribe Amphineuriinae, and four genera (Beaumontia, Ceropegia, Hoya, and Stephanotis) were not resolved as monophyletic. Our work sheds light on the backbone phylogenetic relationships in the family Apocynaceae and offers insights into the evolution of Apocynaceae plastomes using the most densely sampled plastome dataset to date.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Cai-Fei Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Wyclif Ochieng Odago
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hui Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jia-Xin Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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12
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Kamra K, Jung J, Kim JH. A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences. FRONTIERS IN PLANT SCIENCE 2023; 14:1066708. [PMID: 36844099 PMCID: PMC9948625 DOI: 10.3389/fpls.2023.1066708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies-Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae-which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (de novo) the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that Watsonia and Gladiolus were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies-Crocoideae, Nivenioideae, and Aristeoideae-shared a common ycf2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of Watsonia within the tribal classification of the subfamily Crocoideae.
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Gaikwad AB, Kaila T, Maurya A, Kumari R, Rangan P, Wankhede DP, Bhat KV. The chloroplast genome of black pepper ( Piper nigrum L.) and its comparative analysis with related Piper species. FRONTIERS IN PLANT SCIENCE 2023; 13:1095781. [PMID: 36714762 PMCID: PMC9878596 DOI: 10.3389/fpls.2022.1095781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Piper nigrum, also known as black pepper, is an economically and ecologically important crop of the genus Piper. It has been titled as the king of spices due to its wide consumption throughout the world. In the present investigation, the chloroplast genome of P. nigrum has been assembled from a whole genome sequence by integrating the short and long reads generated through Illumina and PacBio platforms, respectively. The chloroplast genome was observed to be 161,522 bp in size, having a quadripartite structure with a large single copy (LSC) region of 89,153 bp and a small single copy (SSC) region of 18,255 bp separated by a copy of inverted repeats (IRs), each 27,057 bp in length. Taking into consideration all the duplicated genes, a total of 131 genes were observed, which included 81 protein-coding genes, 37 tRNAs, 4 rRNAs, and 1 pseudogene. Individually, the LSC region consisted of 83 genes, the SSC region had 13 genes, and 18 genes were present in each IR region. Additionally, 216 SSRs were detected and 11 of these were validated through amplification in 12 species of Piper. The features of the chloroplast genome have been compared with those of the genus Piper. Our results provide useful insights into evolutionary and molecular studies of black pepper which will contribute to its further genetic improvement and breeding.
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Affiliation(s)
- Ambika Baldev Gaikwad
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Tanvi Kaila
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ratna Kumari
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Parimalan Rangan
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dhammaprakash Pandhari Wankhede
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - K. V. Bhat
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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14
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A Large Intergenic Spacer Leads to the Increase in Genome Size and Sequential Gene Movement around IR/SC Boundaries in the Chloroplast Genome of Adiantum malesianum (Pteridaceae). Int J Mol Sci 2022; 23:ijms232415616. [PMID: 36555263 PMCID: PMC9778900 DOI: 10.3390/ijms232415616] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Expansion and contraction (ebb and flow events) of inverted repeat (IR) boundaries occur and are generally considered to be major factors affecting chloroplast (cp) genome size changes. Nonetheless, the Adiantum malesianum cp genome does not seem to follow this pattern. We sequenced, assembled and corrected the A. flabellulatum and A. malesianum cp genomes using the Illumina NovaSeq6000 platform, and we performed a comparative genome analysis of six Adiantum species. The results revealed differences in the IR/SC boundaries of A. malesianum caused by a 6876 bp long rpoB-trnD-GUC intergenic spacer (IGS) in the LSC. This IGS may create topological tension towards the LSC/IRb boundary in the cp genome, resulting in a sequential movement of the LSC genes. Consequently, this leads to changes of the IR/SC boundaries and may even destroy the integrity of trnT-UGU, which is located in IRs. This study provides evidence showing that it is the large rpoB-trnD-GUC IGS that leads to A. malesianum cp genome size change, rather than ebb and flow events. Then, the study provides a model to explain how the rpoB-trnD-GUC IGS in LSC affects A. malesianum IR/SC boundaries. Moreover, this study also provides useful data for dissecting the evolution of cp genomes of Adiantum. In future research, we can expand the sample to Pteridaceae to test whether this phenomenon is universal in Pteridaceae.
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15
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Yang Y, Jia Y, Zhao Y, Wang Y, Zhou T. Comparative chloroplast genomics provides insights into the genealogical relationships of endangered Tetraena mongolica and the chloroplast genome evolution of related Zygophyllaceae species. Front Genet 2022; 13:1026919. [PMID: 36568371 PMCID: PMC9773207 DOI: 10.3389/fgene.2022.1026919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
A comprehensive understanding of genetic background for rare species will provide an important theoretical basis for the future species management, monitoring and conservation. Tetraena mongolica is restrictedly distributed in the western Ordos plateau of China and has been listed as a national protected plant. We generated 13 chloroplast (cp) genomes of T. mongolica (size range of 106,062-106,230 bp) and conducted a series of comparative analyses of six Zygophyllaceae cp genomes. T. mongolica cp genome exhibited a quadripartite structure with drastically reduced inverted repeats (IRs, 4,315 bp) and undergone the loss of a suit of ndh genes and a copy of rRNAs. Furthermore, all the T. mongolica populations were divided into two genetic groups based on complete cp phylogenomics. In addition, notably variable genome size, gene order and structural changes had been observed among the six Zygophyllaceae cp genomes. Overall, our findings provide insights into the cp genome evolution mode and intraspecific relationships of T. mongolica, and provide a molecular basis for scientific conservation of this endangered plant.
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Affiliation(s)
- Yanci Yang
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China
| | - Yun Jia
- Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an, Shaanxi, China
| | - Yanling Zhao
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China
| | - Yonglong Wang
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China,*Correspondence: Yonglong Wang, ; Tao Zhou,
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, Shaanxi, China,*Correspondence: Yonglong Wang, ; Tao Zhou,
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16
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Xiang YL, Jin XJ, Shen C, Cheng XF, Shu L, Zhu RL. New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes. Cladistics 2022; 38:649-662. [PMID: 35779275 DOI: 10.1111/cla.12513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 01/31/2023] Open
Abstract
Marchantiopsida (complex thalloid liverworts) are one of the earliest lineages of embryophytes (land plants), and well-known for their air pores and chambers, pegged rhizoids, and absence of organellular RNA editing sites. Despite their importance to an understanding of early embryophyte evolution, many key nodes within this class remain poorly resolved, owing to the paucity of genetic loci previously available for phylogenetic analyses. Here, we sequenced 54 plastomes, representing 28 genera, nearly all families, and all orders of Marchantiopsida. Based on these plastomes, we present a hypothesis of deep relationships within the class, and make the first investigations of gene contents and synteny. Overall, the Marchantiopsida plastomes were well-conserved, with the exception of the genus Cyathodium that has plastomes with higher GC content, fewer single sequence repeats (SSRs), and more structural variations, implying that this genus might possess RNA editing sites. Abundant repetitive elements and six highly divergent regions were identified as suitable for future infrafamilial taxonomic studies. The phylogenetic topology of Sphaerocarpales, Neohodgsoniales and Blasiales within Marchantiopsida was essentially congruent with previous studies but generally we obtained higher support values. Based on molecular evidence and previous morphological studies, we include Lunulariales in Marchantiales and suggest the retention of narrowed delimitation of monotypic families. The phylogenetic relationships within Marchantiales were better resolved, and 13 monophyletic families were recovered. Our analyses confirmed that the loss of intron 2 of ycf3 is a synapomorphy of Marchantiidae. Finally, we propose a new genus, Asterellopsis (Aytoniaceae), and present an updated classification of Marchantiopsida. The highly supported phylogenetic backbone provided here establishes a framework for future comparative and evolutionary studies of the complex thalloid liverworts.
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Affiliation(s)
- You-Liang Xiang
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xin-Jie Jin
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Chao Shen
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xia-Fang Cheng
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lei Shu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rui-Liang Zhu
- Bryology Laboratory, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,Shanghai Institute of Eco-Chongming (SIEC), Shanghai, 200062, China.,Tiantong National Station of Forest Ecosystem, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, 200241, China
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17
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Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae. Sci Rep 2022; 12:15800. [PMID: 36138079 PMCID: PMC9500069 DOI: 10.1038/s41598-022-19812-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Petrocodon and Primulina are two characteristic genera of Gesneriaceae that exhibit remarkable species and floral diversity, and high endemism across the Sino-Vietnamese Limestone Karsts. To better understand the evolution of limestone gesneriad plastomes, we report nine complete plastomes of seven Primulina and two Petrocodon which have never been assembled before. The newly generated plastomes range from 152,323 to 153,786 bp in size and display a typical quadripartite structure. To further explore the plastome evolution across Gesneriaceae, we assembled five additional plastomes from public reads data and incorporated 38 complete Gesneriaceae plastomes available online into comparative and phylogenomic analyses. The comparison of 52 Gesneriaceae plastomes reveals that not only Primulina and Petrocodon but all gesneriad genera analyzed are highly conserved in genome size, genome structure, gene contents, IR boundary configurations, and codon usage bias. Additionally, sliding window analyses were implemented across alignments of Primulina and Petrocodon for identifying highly variable regions, providing informative markers for future studies. Meanwhile, the SSRs and long repeats of Gesneriaceae plastomes were characterized, serving as useful data in studying population and repetitive sequence evolutions. The results of plastome phylogenetics represent a preliminary but highly resolved maternal backbone genealogy of Primulina and the Old World subtribes of Gesneriaceae.
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18
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Könyves K, Bilsborrow J, Christodoulou MD, Culham A, David J. Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq. PeerJ 2021; 9:e12400. [PMID: 34824912 PMCID: PMC8592052 DOI: 10.7717/peerj.12400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.
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Affiliation(s)
- Kálmán Könyves
- Royal Horticultural Society Garden Wisley, Woking, United Kingdom
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Jordan Bilsborrow
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | | | - Alastair Culham
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - John David
- Royal Horticultural Society Garden Wisley, Woking, United Kingdom
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19
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Yoo MJ, Jin DP, Lee HO, Lim CE. Complete Plastome of Three Korean Asarum (Aristolochiaceae): Confirmation Tripartite Structure within Korean Asarum and Comparative Analyses. PLANTS (BASEL, SWITZERLAND) 2021; 10:2056. [PMID: 34685866 PMCID: PMC8540983 DOI: 10.3390/plants10102056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022]
Abstract
The genus Asarum (Aristolochiaceae) is a well-known resource of medicinal and ornamental plants. However, the taxonomy of Korean Asarum is ambiguous due to their considerable morphological variations. Previously, a unique plastome structure has been reported from this genus. Therefore, we investigated the structural change in the plastomes within three Korean Asarum species and inferred their phylogenetic relationships. The plastome sizes of Asarum species assembled here range from 190,168 to 193,356 bp, which are longer than a typical plastome size (160 kb). This is due to the incorporation and duplication of the small single copy into the inverted repeat, which resulted in a unique tripartite structure. We first verified this unique structure using the Illumina Miseq and Oxford Nanopore MinION platforms. We also investigated the phylogeny of 26 Aristolochiaceae species based on 79 plastid protein-coding genes, which supports the monophyly of Korean Asarum species. Although the 79 plastid protein-coding gene data set showed some limitations in supporting the previous classification, it exhibits its effectiveness in delineating some sections and species. Thus, it can serve as an effective tool for resolving species-level phylogeny in Aristolochiaceae. Last, we evaluated variable sites and simple sequence repeats in the plastome as potential molecular markers for species delimitation.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA;
| | - Dong-Pil Jin
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon 22689, Korea;
| | - Hyun-Oh Lee
- Phyzen Inc., 13 Seongnam-daero, 331 beon-gil, Bundang-gu, Seongnam-si 13558, Korea;
| | - Chae Eun Lim
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon 22689, Korea;
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20
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Sun J, Wang Y, Garran TA, Qiao P, Wang M, Yuan Q, Guo L, Huang L. Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources. Front Genet 2021; 12:721022. [PMID: 34603384 PMCID: PMC8479170 DOI: 10.3389/fgene.2021.721022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022] Open
Abstract
Leonurus cardiaca has a long history of use in western herbal medicine and is applied for the treatment of gynaecological conditions, anxiety, and heart diseases. Because of its botanical relationship to the primary Chinese species, L. japonicus, and extensive medical indications that go beyond the traditional indications for the Chinese species, it is a promising medicinal resource. Therefore, the features of genetic diversity and variability in the species have been prioritized. To explore these issues, we sequenced the chloroplast genomes of 22 accessions of L. cardiaca from different geographical locations worldwide using high-throughput sequencing. The results indicate that L. cardiaca has a typical quadripartite structure and range from 1,51,236 bp to 1,51,831 bp in size, forming eight haplotypes. The genomes all contain 114 distinct genes, including 80 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Comparative analysis showed abundant diversity of single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) in 22 accessions. Codon usage showed highly similar results for L. cardiaca species. The phylogenetic and network analysis indicated 22 accessions forming four clades that were partly related to the geographical distribution. In summary, our study highlights the advantage of chloroplast genome with large data sets in intraspecific diversity evaluation and provides a new tool to facilitate medicinal plant conservation and domestication.
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Affiliation(s)
- Jiahui Sun
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Thomas Avery Garran
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ping Qiao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Academician workstation, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Mengli Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qingjun Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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21
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Wu S, Chen J, Li Y, Liu A, Li A, Yin M, Shrestha N, Liu J, Ren G. Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives. BMC PLANT BIOLOGY 2021; 21:421. [PMID: 34521343 PMCID: PMC8438982 DOI: 10.1186/s12870-021-03202-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/31/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. RESULTS We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. CONCLUSIONS Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.
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Affiliation(s)
- Shuang Wu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jinyuan Chen
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ao Li
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education &State Key Lab of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.
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22
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Lee C, Ruhlman TA, Jansen RK. Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes. Genome Biol Evol 2021; 12:641-655. [PMID: 32282915 PMCID: PMC7426004 DOI: 10.1093/gbe/evaa076] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) of land plants have a conserved quadripartite structure in a gene-dense unit genome consisting of a large inverted repeat that separates two single copy regions. Recently, alternative plastome structures were suggested in Geraniaceae and in some conifers and Medicago the coexistence of inversion isomers has been noted. In this study, plastome sequences of two Cyperaceae, Eleocharis dulcis (water chestnut) and Eleocharis cellulosa (gulf coast spikerush), were completed. Unlike the conserved plastomes in basal groups of Poales, these Eleocharis plastomes have remarkably divergent features, including large plastome sizes, high rates of sequence rearrangements, low GC content and gene density, gene duplications and losses, and increased repetitive DNA sequences. A novel finding among these features was the unprecedented level of heteroplasmy with the presence of multiple plastome structural types within a single individual. Illumina paired-end assemblies combined with PacBio single-molecule real-time sequencing, long-range polymerase chain reaction, and Sanger sequencing data identified at least four different plastome structural types in both Eleocharis species. PacBio long read data suggested that one of the four E. dulcis plastome types predominates.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin.,Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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23
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Guo YY, Yang JX, Bai MZ, Zhang GQ, Liu ZJ. The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions. BMC PLANT BIOLOGY 2021; 21:248. [PMID: 34058997 DOI: 10.21203/rs.3.rs-257472/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/20/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. RESULTS Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 - 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. CONCLUSIONS We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.
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Affiliation(s)
- Yan-Yan Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jia-Xing Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ming-Zhu Bai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization At College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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24
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Guo YY, Yang JX, Bai MZ, Zhang GQ, Liu ZJ. The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions. BMC PLANT BIOLOGY 2021; 21:248. [PMID: 34058997 PMCID: PMC8165784 DOI: 10.1186/s12870-021-03053-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/20/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. RESULTS Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 - 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. CONCLUSIONS We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.
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Affiliation(s)
- Yan-Yan Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jia-Xing Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ming-Zhu Bai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization At College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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25
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Rhie YH, Lee SY, Walck JL, Hidayati SN. Seed dormancy and germination of Asarum sieboldii, a disjunct relict species in East Asia. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:300-306. [PMID: 33289269 DOI: 10.1111/plb.13224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Disjunct species in the same genus are a common feature of the flora in the temperate forests of East Asia and eastern North America. This study aimed to evaluate whether the kind of seed dormancy was maintained after species in the genus Asarum (Aristolochiaceae) were separated from their common ancestor. We classified the seed dormancy of Asarum sieboldii, an East Asian species, based on a phenology study and experiments in controlled temperature conditions, and then compared it to that of the previously studied A. canadense, an eastern North American species. The underdeveloped embryo of A. sieboldii grew and germinated (radicle emergence) in autumn but shoot emergence did not occur until the following spring. The seeds of A. sieboldii had deep simple epicotyl morphophysiological dormancy because the seeds with emerged radicle required a relatively long period of cold stratification to break epicotyl dormancy and produce a shoot. Although the seed of A. sieboldii had weaker radicle dormancy and stronger epicotyl dormancy compared to A. canadense, the kind of seed dormancy was the same for the two species. The trait of seed dormancy was inherited from a shared common ancestor and maintained in populations well after the two species (or their ancestors) separated. However, quantitative differences in temperature requirements for radicle and shoot emergence suggest the possibility of adaptation to the environment.
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Affiliation(s)
- Y H Rhie
- Department of Horticulture and Forestry, Pai Chai University, Daejeon, Korea
| | - S Y Lee
- Division of Horticulture & Medicinal Plant, Andong National University, Andong, Korea
| | - J L Walck
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - S N Hidayati
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
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26
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Choi KS, Ha YH, Gil HY, Choi K, Kim DK, Oh SH. Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. PLANTS (BASEL, SWITZERLAND) 2021; 10:397. [PMID: 33669616 PMCID: PMC7922562 DOI: 10.3390/plants10020397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
Previous studies on the chloroplast genome in Clematis focused on the chloroplast structure within Anemoneae. The chloroplast genomes of Cleamtis were sequenced to provide information for studies on phylogeny and evolution. Two Korean endemic Clematis chloroplast genomes (Clematis brachyura and C. trichotoma) range from 159,170 to 159,532 bp, containing 134 identical genes. Comparing the coding and non-coding regions among 12 Clematis species revealed divergent sites, with carination occurring in the petD-rpoA region. Comparing other Clematis chloroplast genomes suggested that Clematis has two inversions (trnH-rps16 and rps4), reposition (trnL-ndhC), and inverted repeat (IR) region expansion. For phylogenetic analysis, 71 protein-coding genes were aligned from 36 Ranunculaceae chloroplast genomes. Anemoneae (Anemoclema, Pulsatilla, Anemone, and Clematis) clades were monophyletic and well-supported by the bootstrap value (100%). Based on 70 chloroplast protein-coding genes, we compared nonsynonymous (dN) and synonymous (dS) substitution rates among Clematis, Anemoneae (excluding Clematis), and other Ranunculaceae species. The average synonymoussubstitution rates (dS)of large single copy (LSC), small single copy (SSC), and IR genes in Anemoneae and Clematis were significantly higher than those of other Ranunculaceae species, but not the nonsynonymous substitution rates (dN). This study provides fundamental information on plastid genome evolution in the Ranunculaceae.
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Affiliation(s)
- Kyoung Su Choi
- Institute of Natural Science, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea;
- Department of Life Sciences, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea
| | - Young-Ho Ha
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
- Department of Life Science, Gachon University, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Hee-Young Gil
- DMZ Botanic Garden, Korea National Arboretum, 916-70, Punchbowl-ro, Haean-myeon, Yanggu, Gangwon-do 24564, Korea;
| | - Kyung Choi
- Research Planning and Coordination Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea;
| | - Dong-Kap Kim
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
| | - Seung-Hwan Oh
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
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27
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Yuan C, Sha X, Xiong M, Zhong W, Wei Y, Li M, Tao S, Mou F, Peng F, Zhang C. Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications. Sci Rep 2021; 11:988. [PMID: 33441833 PMCID: PMC7806627 DOI: 10.1038/s41598-020-80225-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.
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Affiliation(s)
- Can Yuan
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Xiufen Sha
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Miao Xiong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Wenjuan Zhong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Yu Wei
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingqian Li
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, Zhejiang, China
| | - Shan Tao
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Fangsheng Mou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China
| | - Fang Peng
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
| | - Chao Zhang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
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28
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Wei N, Pérez-Escobar OA, Musili PM, Huang WC, Yang JB, Hu AQ, Hu GW, Grace OM, Wang QF. Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region. FRONTIERS IN PLANT SCIENCE 2021; 12:712064. [PMID: 34421963 PMCID: PMC8372406 DOI: 10.3389/fpls.2021.712064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 05/09/2023]
Abstract
With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.
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Affiliation(s)
- Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Paul M. Musili
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Wei-Chang Huang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Olwen M. Grace
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- *Correspondence: Olwen M. Grace,
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Qing-Feng Wang,
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29
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Guo YY, Yang JX, Li HK, Zhao HS. Chloroplast Genomes of Two Species of Cypripedium: Expanded Genome Size and Proliferation of AT-Biased Repeat Sequences. FRONTIERS IN PLANT SCIENCE 2021; 12:609729. [PMID: 33633763 PMCID: PMC7900419 DOI: 10.3389/fpls.2021.609729] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/20/2021] [Indexed: 05/07/2023]
Abstract
The size of the chloroplast genome (plastome) of autotrophic angiosperms is generally conserved. However, the chloroplast genomes of some lineages are greatly expanded, which may render assembling these genomes from short read sequencing data more challenging. Here, we present the sequencing, assembly, and annotation of the chloroplast genomes of Cypripedium tibeticum and Cypripedium subtropicum. We de novo assembled the chloroplast genomes of the two species with a combination of short-read Illumina data and long-read PacBio data. The plastomes of the two species are characterized by expanded genome size, proliferated AT-rich repeat sequences, low GC content and gene density, as well as low substitution rates of the coding genes. The plastomes of C. tibeticum (197,815 bp) and C. subtropicum (212,668 bp) are substantially larger than those of the three species sequenced in previous studies. The plastome of C. subtropicum is the longest one of Orchidaceae to date. Despite the increase in genome size, the gene order and gene number of the plastomes are conserved, with the exception of an ∼75 kb large inversion in the large single copy (LSC) region shared by the two species. The most striking is the record-setting low GC content in C. subtropicum (28.2%). Moreover, the plastome expansion of the two species is strongly correlated with the proliferation of AT-biased non-coding regions: the non-coding content of C. subtropicum is in excess of 57%. The genus provides a typical example of plastome expansion induced by the expansion of non-coding regions. Considering the pros and cons of different sequencing technologies, we recommend hybrid assembly based on long and short reads applied to the sequencing of plastomes with AT-biased base composition.
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30
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Liao M, Gao XF, Zhang JY, Deng HN, Xu B. Comparative Chloroplast Genomics of Sophora Species: Evolution and Phylogenetic Relationships in the Early-Diverging Legume Subfamily Papilionoideae (Fabaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:778933. [PMID: 34975964 PMCID: PMC8716937 DOI: 10.3389/fpls.2021.778933] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/08/2021] [Indexed: 05/04/2023]
Abstract
The taxonomy and evolutionary history of Sophora L., a genus with high economic and medicinal value, remain uncertain due to the absence of genetic resource (especially in China) and low polymorphism of molecular markers. Our aim was to elucidate the molecular evolution and phylogenetic relationships in chloroplast genomes of Sophora species in the early-diverging legume subfamily Papilionoideae (Fabaceae). We reported nine Sophora chloroplast genome from China using Illumina sequencing. We performed a series of analyses with previously published genomes of Sophora species to investigate their genomic characteristics, identified simple sequence repeats, large repeat sequences, tandem repeats, and highly polymorphic loci. The genomes were 152,953-158,087 bp in length, and contained 111-113 unique genes, including 76-78 protein coding, 31 tRNA, and 4 rRNA. The expansion of inverted repeat boundary of Sophora resulted in rps12 entering into the LSC region and loss of trnT-CGU gene in some species. Also, we found an approximately 23 kb inversion between trnC-GCA and trnF-GAA within the genus. In addition, we identified seven highly polymorphic loci (pi (π) > 0.035) suitable for inferring the phylogeny of Sophora species. Among these, three regions also co-occurred with large repeat sequences and support use of repeats as a proxy for the identification of polymorphic loci. Based on whole chloroplast genome and protein-coding sequences data-set, a well-supported phylogenetic tree of Sophora and related taxa showed that this genus is monophyletic, but sect. Disamaea and sect. Sophora, are incongruent with traditional taxonomic classifications based on fruit morphology. Our finding provides significant genetic resources to support further investigation into the phylogenetic relationship and evolution of the genus Sophora.
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Affiliation(s)
- Min Liao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jun-Yi Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Heng-Ning Deng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- *Correspondence: Bo Xu,
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Kang JS, Zhang HR, Wang YR, Liang SQ, Mao ZY, Zhang XC, Xiang QP. Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1657-1672. [PMID: 33073395 DOI: 10.1111/tpj.15028] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/21/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Plastids and mitochondria are endosymbiotic organelles that store genetic information. The genomes of these organelles generally exhibit contrasting patterns regarding genome architecture and genetic content. However, they have similar genetic features in Selaginellaceae, and little is known about what causes parallel evolution. Here, we document the multipartite plastid genomes (plastomes) and the highly divergent mitochondrial genomes (mitogenomes) from spikemoss obtained by combining short- and long-reads. The 188-kb multipartite plastome has three ribosomal operon copies in the master genomic conformation, creating the alternative subgenomic conformation composed of 110- and 78-kb subgenomes. The long-read data indicated that the two different genomic conformations were present in almost equal proportions in the plastomes of Selaginella nipponica. The mitogenome of S. nipponica was assembled into 27 contigs with a total size of 110 kb. All contigs contained directly arranged repeats at both ends, which introduced multiple conformations. Our results showed that plastomes and mitogenomes share high tRNA losses, GC-biased nucleotides, elevated substitution rates and complicated organization. The exploration of nuclear-encoded organelle DNA replication, recombination and repair proteins indicated that, several single-targeted proteins, particularly plastid-targeted recombinase A1, have been lost in Selaginellaceae; conversely, the dual-targeted proteins remain intact. According to the reported function of recombinase A1, we propose that the plastomes of spikemoss often fail to pair homologous sequences during recombination, and the dual-targeted proteins play a key role in the convergent genetic features of plastomes and mitogenomes. Our results provide a distinctive evolutionary pattern of the organelle genomes in Selaginellaceae and evidence of their convergent evolution.
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Affiliation(s)
- Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ya-Rong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Si-Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Yuan Mao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Mohanta TK, Mishra AK, Khan A, Hashem A, Abd_Allah EF, Al-Harrasi A. Gene Loss and Evolution of the Plastome. Genes (Basel) 2020; 11:E1133. [PMID: 32992972 PMCID: PMC7650654 DOI: 10.3390/genes11101133] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
Chloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203-156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.
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Affiliation(s)
- Tapan Kumar Mohanta
- Biotech and Omics Laboratory, Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Oman;
| | | | - Adil Khan
- Biotech and Omics Laboratory, Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Oman;
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Giza 12511, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia;
| | - Ahmed Al-Harrasi
- Natural Product Laboratory, Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Oman
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Barrett CF. Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L. PeerJ 2020; 8:e9315. [PMID: 32587799 PMCID: PMC7304433 DOI: 10.7717/peerj.9315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/17/2020] [Indexed: 12/12/2022] Open
Abstract
Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
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Li Z, Ma X, Wen Y, Chen S, Jiang Y, Jin X. Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region. PeerJ 2020; 8:e9157. [PMID: 32551191 PMCID: PMC7292021 DOI: 10.7717/peerj.9157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/18/2020] [Indexed: 11/20/2022] Open
Abstract
Mycoheterotrophic plants are highly specialized species able to acquire organic carbon from symbiotic fungi, with relaxed dependence on photosynthesis for carbon fixation. The relaxation of the functional constraint of photosynthesis and thereby the relaxed selective pressure on functional photosynthetic genes usually lead to substantial gene loss and a highly degraded plastid genome in heterotrophs. In this study, we sequenced and analyzed the plastome of the eudicot Exacum paucisquama, providing the first plastid genome of a mycoheterotroph in the family Gentianaceae to date. The E. paucisquama plastome was 44,028 bp in length, which is much smaller than the plastomes of autotrophic eudicots. Although the E. paucisquama plastome had a quadripartite structure, a distinct boundary shift was observed in comparison with the plastomes of other eudicots. We detected extensive gene loss and only 21 putative functional genes (15 protein-coding genes, four rRNA genes and two tRNA genes). Our results provide valuable information for comparative evolutionary analyses of plastomes of heterotrophic species belonging to different phylogenetic groups.
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Affiliation(s)
- Zhanghai Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yi Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sisi Chen
- Nanchang University, Nanchang, China
| | - Yan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (CAS-SEABRI), Xishuangbanna, China
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Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae). Mol Phylogenet Evol 2020; 145:106729. [DOI: 10.1016/j.ympev.2019.106729] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 01/02/2023]
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Jin DP, Choi IS, Choi BH. Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae). PLoS One 2019; 14:e0218743. [PMID: 31233545 PMCID: PMC6590825 DOI: 10.1371/journal.pone.0218743] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/08/2019] [Indexed: 11/23/2022] Open
Abstract
Recent plastid genome (plastome) studies of legumes (family Fabaceae) have shown that this family has undergone multiple atypical plastome evolutions from each of the major clades. The tribe Desmodieae belongs to the Phaseoloids, an important but systematically puzzling clade within Fabaceae. In this study, we investigated the plastome evolution of Desmodieae and analyzed its phylogenetic signaling. We sequenced six complete plastomes from representative members of Desmodieae and from its putative sister Phaseoloid genus Mucuna. Those genomes contain 128 genes and range in size from 148,450 to 153,826 bp. Analyses of gene and intron content revealed similar characters among the members of Desmodieae and Mucuna. However, there were also several distinct characters identified. The loss of the rpl2 intron was a feature shared between Desmodieae and Mucuna, whereas the loss of the rps12 intron was specific to Desmodieae. Likewise, gene loss of rps16 was observed in Mucuna but not in Desmodieae. Substantial sequence variation of ycf4 was detected from all the sequenced plastomes, but pseudogenization was restricted to the genus Desmodium. Comparative analysis of gene order revealed a distinct plastome conformation of Desmodieae compared with other Phaseoloid legumes, i.e., an inversion of an approximately 1.5-kb gene cluster (trnD-GUC, trnY-GUA, and trnE-UUC). The inversion breakpoint suggests that this event was mediated by the recombination of an 11-bp repeat motif. A phylogenetic analysis based on the plastome-scale data set found the tribe Desmodieae is a highly supported monophyletic group nested within the paraphyletic Phaseoleae, as has been found in previous phylogenetic studies. Two subtribes (Desmodiinae and Lespedezinae) of Desmodieae were also supported as monophyletic groups. Within the subtribe Lespedezinae, Lespedeza is closer to Kummerowia than Campylotropis.
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Affiliation(s)
- Dong-Pil Jin
- Department of Biological Sciences, Inha University, Michuhol-gu, Incheon, Republic of Korea
| | - In-Su Choi
- Department of Biological Sciences, Inha University, Michuhol-gu, Incheon, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, Michuhol-gu, Incheon, Republic of Korea
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Sablok G, Amiryousefi A, He X, Hyvönen J, Poczai P. Sequencing the Plastid Genome of Giant Ragweed ( Ambrosia trifida, Asteraceae) From a Herbarium Specimen. FRONTIERS IN PLANT SCIENCE 2019; 10:218. [PMID: 30873197 PMCID: PMC6403193 DOI: 10.3389/fpls.2019.00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.
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Affiliation(s)
- Gaurav Sablok
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Xiaolan He
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species. Int J Mol Sci 2019; 20:ijms20051045. [PMID: 30823362 PMCID: PMC6429227 DOI: 10.3390/ijms20051045] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 11/16/2022] Open
Abstract
Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.
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Ha YH, Choi KS, Choi K. Characterization of complete chloroplast genome of endemic species of Korea Peninsular, Salvia chanryoenica (Lamiaceae). Mitochondrial DNA B Resour 2018; 3:992-993. [PMID: 33474391 PMCID: PMC7800916 DOI: 10.1080/23802359.2018.1495115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Salvia chanryoenica is an endemic species, which locates on the ridges of mountains in South Korea. In this study, we determined the complete chloroplast (cp) genome sequence of S. chanryoenica; cp genome of S. chanryoenica is 151,689 bp in length and consists of a large (82,903 bp) and small (17,634 bp) single-copy regions, separated by a pair of identical inverted repeats (25,576 bp). This genome contains unique 79 protein-coding genes, 30 tRNA, and 4 rRNA. The gene order and organization of the S. chanryoenica are consistent with those of other Lamiaceae cp genomes. The overall GC content of the whole genome was 37.9%. Phylogenetic tree constructed based on 71 protein-coding genes demonstrated a sister relationship within genus Salvia.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum of the Korea Forest Service, Pochen, 1186, Korea
| | - Kyoung Su Choi
- Division of Forest Biodiversity, Korea National Arboretum of the Korea Forest Service, Pochen, 1186, Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum of the Korea Forest Service, Pochen, 1186, Korea
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