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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [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: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
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Zhao M, Wu Y, Ren Y. Complete Chloroplast Genome Sequence Structure and Phylogenetic Analysis of Kohlrabi ( Brassica oleracea var. gongylodes L.). Genes (Basel) 2024; 15:550. [PMID: 38790180 PMCID: PMC11120933 DOI: 10.3390/genes15050550] [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: 04/04/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes were identified, including 87 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The base composition analysis showed that the overall GC content was 36.36% of the complete chloroplast genome sequence. Relative synonymous codon usage frequency (RSCU) analysis showed that most codons with values greater than 1 ended with A or U, while most codons with values less than 1 ended with C or G. Thirty-five scattered repeats were identified and most of them were distributed in the large single-copy (LSC) region. A total of 290 simple sequence repeats (SSRs) were found and 188 of them were distributed in the LSC region. Phylogenetic relationship analysis showed that five Brassica oleracea subspecies were clustered into one group and the kohlrabi chloroplast genome was closely related to that of B. oleracea var. botrytis. Our results provide a basis for understanding chloroplast-dependent metabolic studies and provide new insight for understanding the polyploidization of Brassicaceae species.
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Affiliation(s)
- Mengliang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Yanxun Wu
- Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, China;
| | - Yanjing Ren
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, China;
- Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Xining 810016, China
- Qinghai Provincial Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
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Hou Y, Zhang Y, Yu J, Wang X. Characteristics of the complete chloroplast genome of Swertia divaricata Harry Sm. (Gentianaceae) and its phylogenetic inference. Mitochondrial DNA B Resour 2023; 8:1132-1136. [PMID: 37928401 PMCID: PMC10621253 DOI: 10.1080/23802359.2023.2270211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 10/07/2023] [Indexed: 11/07/2023] Open
Abstract
Swertia divaricata Harry Sm., 1965, (Gentianaceae) is a perennial herb endemic to Northwest Yunnan, China, belonging to the species-rich genus Swertia. It possesses unique morphological features but its systematic position remains uncertain. To determine its phylogenetic placement, the complete plastid genome of S. divaricata was assembled utilizing high-throughput sequencing data. The genome is circular, spanning 152,073 bp, and comprises a large single-copy (LSC) region of 82,470 bp, a small single-copy (SSC) region of 18,153 bp, and two inverted repeats (IR) regions, each 25,725 bp. A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The plastome of S. divaricata exhibits a structure and gene composition highly similar to those of other Swertia plastomes. Phylogenetic analysis indicated that S. divaricata is closely related to S. erythrosticta, sister to a subclade comprising species from sections Swertia and Apterae. The plastome sequence described herein constitutes a valuable contribution to phylogenetic and evolutionary research on Swertia.
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Affiliation(s)
- Yingying Hou
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Integrated Traditional Chinese and Western Medicine, The Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Yulong Zhang
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Integrated Traditional Chinese and Western Medicine, The Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Jing Yu
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinjie Wang
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Sun X, Zhan Y, Li S, Liu Y, Fu Q, Quan X, Xiong J, Gang H, Zhang L, Qi H, Wang A, Huo J, Qin D, Zhu C. Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant ( Ribes nigrum), red and white currant ( Ribes rubrum), and gooseberry ( Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae. PeerJ 2023; 11:e16272. [PMID: 37842068 PMCID: PMC10573389 DOI: 10.7717/peerj.16272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Background Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding. Methods The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed. Results The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species.
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Affiliation(s)
- Xinyu Sun
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ying Zhan
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Songlin Li
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yu Liu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Qiang Fu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xin Quan
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jinyu Xiong
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Huixin Gang
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Lijun Zhang
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Heilongjiang Institute of Green Food Science, Harbin, Heilongjiang, China
| | - Huijuan Qi
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Heilongjiang Institute of Green Food Science, Harbin, Heilongjiang, China
| | - Aoxue Wang
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Junwei Huo
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Dong Qin
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Chenqiao Zhu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
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Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships. Mol Genet Genomics 2023; 298:399-411. [PMID: 36592219 DOI: 10.1007/s00438-022-01991-2] [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: 11/08/2021] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Species in Gentiana section Cruciata are important alpine plants with a center of diversity and speciation in Qinghai-Tibet Plateau (QTP), and some of these species are sympatrically distributed in northeastern QTP. Studies on genome features and natural selection signatures of sympatric species in section Crucata have been impeded by a lack of genomic resources. Here, we showed transcript characterizations and molecular footprints of selection effects on G. straminea, G. dahurica and G. officinalis based on the comparative transcriptome. A total of 62.97 Gb clean reads were obtained with unigene numbers per species ranging from 141,819 to 236,408 after assembly. We found that these three species had similar distribution of functional categories in different databases, and key enzyme-encoding genes involved in the iridoids biosynthesis were also obtained. The selective pressure analyses indicated that most paired orthologs between these three species were subject to negative selection, and only a low proportion of the orthologs that underwent positive selection were detected. We found that some positive selected genes were involved in "catalytic activity", "metabolic process", "response to stimulus" and "response to stress". Besides, large numbers of SSR primer pairs with transferabilities were successfully designed based on the available transcriptome datasets of three Gentiana species. The phylogenetic relationships reconstructed based on 352 single-copy nuclear genes provided a rough phylogenetic framework for this genus and confirmed the monophyly of section Cruciata. Our study not only provides insights for the natural selection effects on sympatric Gentiana species, but also enhances future genetic breeding or evolutionary studies on Qinjiao species.
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Mao J, Liang Y, Wang X, Zhang D. Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization. BMC PLANT BIOLOGY 2023; 23:101. [PMID: 36800941 PMCID: PMC9940437 DOI: 10.1186/s12870-023-04088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences. RESULTS The plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens. CONCLUSION G. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.
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Affiliation(s)
- Jiuyang Mao
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Yuze Liang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China.
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali, 671000, Yunnan, China.
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Yuan R, Ma X, Zhang Z, Gornall RJ, Wang Y, Chen S, Gao Q. Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae). Ecol Evol 2023; 13:e9694. [PMID: 36620410 PMCID: PMC9817205 DOI: 10.1002/ece3.9694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/28/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Comprising ca. 200 species, Saxifraga sect. Ciliatae is the most species-rich section of Saxifraga s.str., whose center of diversity is in the Tibeto-Himalayan region. The infra-sectional classification of sect. Ciliatae is still in debate due to the high level of species richness, as well as remarkable variations of habitat, morphology, physiology and life cycles. Subdivisions of this section proposed in various taxonomic systems have not been adequately tested in previous phylogenetic studies, partly due to low taxonomic sampling density, but also to the use of few DNA markers. In order to achieve a more robust infra-sectional classification of sect. Ciliatae, complete chloroplast genomes of 94 taxa from this section were analyzed, of which 93 were newly sequenced, assembled and annotated. The length of the 94 plastomes of sect. Ciliatae taxa range from 143,479 to 159,938 bp, encoding 75 to 79 unique protein-coding genes (PCGs). Analyses of the 94 plastomes revealed high conservation in structural organization, gene arrangement, and gene content. Gene loss and changes of IR boundaries were detected but in extremely low frequency. The molecular phylogenetic tree from concatenated PCGs and complete chloroplast genome sequences exhibited high resolution and support values and confirms that sect. Ciliatae is monophyletic. Three well-supported clades were revealed within the section that agree relatively well with the subsectional taxonomy of Gornall (1987), but some minor modifications should be made. Firstly, the monotypic subsection Cinerascentes should be abandoned and its constituent species, S. cinerascens, assigned to subsect. Gemmiparae. Secondly, subsections Rosulares and Serpyllifoliae should be merged and become subsect. Rosulares. Section Ciliatae thus comprises: subsect. Hirculoideae Engl. & Irmsch.; subsect. Rosulares Gornall; subsect. Gemmiparae Engl. & Irmsch.; subsect. Flagellares (C. B. Clarke) Engl. & Irmsch. and subsect. Hemisphaericae (Engl. & Irmsch.) Gornall.
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Affiliation(s)
- Rui Yuan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina,University of Chinese Academy of SciencesBeijingChina
| | - Xiaolei Ma
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina,University of Chinese Academy of SciencesBeijingChina
| | - Zhuoxin Zhang
- College of Forestry and Landscape ArchitectureSouth China Agricultual UniversityGuanzhouChina
| | | | - Yongcui Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina,Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
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Yu J, Fu P, Sun S. Complete plastid genome of Gentiana zollingeri Fawcett (Gentianaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:2063-2066. [PMCID: PMC9744209 DOI: 10.1080/23802359.2022.2152644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Gentiana zollingeri Fawcett (Gentianaceae) belongs to the most species-rich section, Chondrophyllae, in the Gentianaceae, but its phylogenetic relationship with other members of this section is unclear. To confirm its phylogenetic position, the complete plastid genome of G. zollingeri was determined and analyzed. The plastome was sequenced using the Illumina HiSeq platform, assembled with GetOrganelle, and annotated with GeSeq. The genome is circular with a length of 130,762 bp. It contains a large single-copy (LSC) region of 74,236 bp, a small single-copy (SSC) region of 10,598 bp, and two inverted repeat (IR) regions of 22,964 bp each. The plastome of G. zollingeri shows considerable structural differences from those of other Gentiana plastomes, such as the absence of the ndh gene. In phylogenetic analyses, section Chondrophyllae, including G. zollingeri and its sisters, formed a long branch sistering with section Cruciata. The plastome sequence described here represents an important contribution to phylogenetic and evolutionary studies on Gentiana.
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Affiliation(s)
- Jing Yu
- Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Pengcheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, China
| | - Shanshan Sun
- School of Life Science, Luoyang Normal University, Luoyang, China,CONTACT Shanshan Sun School of Life Science, Luoyang Normal University, Luoyang, China
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Fu P, Favre A, Wang R, Huang Y, Sun S. Between allopatry and secondary contact: differentiation and hybridization among three sympatric Gentiana species in the Qinghai-Tibet Plateau. BMC PLANT BIOLOGY 2022; 22:504. [PMID: 36307765 PMCID: PMC9615307 DOI: 10.1186/s12870-022-03879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Mountains of the world host a significant portion of all terrestrial biodiversity, and the region of the Qinghai-Tibet Plateau (QTP) stands as one of the most remarkable mountain regions on Earth. Because many explosive radiations occurred there, the QTP is a natural laboratory which is ideal to investigate patterns and processes linked to speciation and diversification. Indeed, understanding how closely related and sympatric species diverged is vital to explore drivers fostering speciation, a topic only rarely investigated in the QTP. By combining genomic and environmental data, we explored the speciation process among three closely related and sympatric species, Gentiana hexaphylla, G. lawrencei and G. veitchiorum in the QTP region. RESULTS Combining genome sizes and cytological data, our results showed that G. hexaphylla and G. veitchiorum are diploid, whereas G. lawrencei is tetraploid. Genetic clustering and phylogenetic reconstruction based on genomic SNPs indicated a clear divergence among the three species. Bayesian clustering, migrant, and D-statistic analyses all showed an obvious signature of hybridization among the three species, in particular between G. lawrencei and both G. hexaphylla and G. veitchiorum in almost all populations. Environmental variables related to precipitation and particularly temperature showed significant differences among the three gentians, and in fact a redundancy analysis confirmed that temperature and precipitation were the major climatic factors explaining the genetic differentiation among the three species. CONCLUSION Our study suggested that ancient hybridization, polyploidization, geological isolation and the evolution of different climatic preferences were all likely to be involved in the divergence of the three Gentiana species, as may be the case for many other taxa in the QTP region.
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Affiliation(s)
- Pengcheng Fu
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Adrien Favre
- Regional nature park of the Trient Valley, La Place 24, 1922, Salvan, Switzerland
| | - Rui Wang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Yizhuo Huang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Shanshan Sun
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China.
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Fu PC, Sun SS, Hollingsworth PM, Chen SL, Favre A, Twyford AD. Population genomics reveal deep divergence and strong geographical structure in gentians in the Hengduan Mountains. FRONTIERS IN PLANT SCIENCE 2022; 13:936761. [PMID: 36092450 PMCID: PMC9453878 DOI: 10.3389/fpls.2022.936761] [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: 05/05/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Understanding the evolutionary and ecological processes driving population differentiation and speciation can provide critical insights into the formation of biodiversity. Here, we examine the link between population genetic processes and biogeographic history underlying the generation of diversity in the Hengduan Mountains (HM), a region harboring a rich and dynamic flora. We used restriction site-associated DNA sequencing to generate 1,907 single-nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing diversification of G. hexaphylla in the HM. We find the G. hexaphylla complex is characterized by geographic genetic structure with clusters corresponding to the South, North and the central HM. Phylogenetic reconstruction and pairwise F ST analyses showed deep differentiation between Southern and Northern populations in the HM. The population in Mount Taibai exhibited the highest genetic similarity to the North HM. Ancestral range estimation indicated that the G. hexaphylla complex originated in the central HM and then diverged in the Pliocene and the Early Pleistocene, before dispersing widely, resulting in the current distinct lineages. Overall, we found deep genomic differentiation in the G. hexaphylla complex corresponds to geographic barriers to dispersal in the HM and highlights a critical role of the uplift of the Daxue Mountains and subsequent climatic fluctuations underlying diversification. The colonization of G. hexaphylla in the Mount Taibai region suggests directional dispersal between the alpine flora of the Qinling Mountains and the HM.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, China
| | | | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History Museum, Frankfurt, Germany
| | - Alex D. Twyford
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
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Fu PC, Chen SL, Sun SS, Favre A. Strong plastid degradation is consistent within section Chondrophyllae, the most speciose lineage of Gentiana. Ecol Evol 2022; 12:e9205. [PMID: 35991284 PMCID: PMC9379351 DOI: 10.1002/ece3.9205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
Recovering phylogenetic relationships in lineages experiencing intense diversification has always been a persistent challenge in evolutionary studies, including in Gentiana section Chondrophyllae sensu lato (s.l.). Indeed, this subcosmopolitan taxon encompasses more than 180 mostly annual species distributed around the world. We sequenced and assembled 22 new plastomes representing 21 species in section Chondrophyllae s.l. In addition to previously released plastome data, our study includes all main lineages within the section. We reconstructed their phylogenetic relationships based on protein‐coding genes and recombinant DNA (rDNA) cistron sequences, and then investigated plastome structural evolution as well as divergence time. Despite an admittedly humble species cover overall, we recovered a well‐supported phylogenetic tree based on plastome data, and found significant discordance between phylogenetic relationships and taxonomic treatments. Our results show that G. capitata and G. leucomelaena diverged early within the section, which is then further divided into two clades. The divergence time estimation showed that section Chondrophyllae s.l. evolved in the second half of the Oligocene. We found that section Chondrophyllae s.l. had the smallest average plastome size (128 KB) in tribe Gentianeae (Gentianaceae), with frequent gene and sequence losses such as the ndh complex and its flanking regions. In addition, we detected both expansion and contraction of the inverted repeat (IR) regions. Our study suggests that plastome degradation parallels the diversification of this group, and illustrates the strong discordance between phylogenetic relationships and taxonomic treatments, which now need to be carefully revised.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University Luoyang P. R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau Biology, Chinese Academy of Sciences Xining P. R. China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University Luoyang P. R. China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History Museum Frankfurt am Main Germany.,Regional Nature Park of the Trient Valley Salvan Switzerland
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12
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Zhao R, Yin S, Xue J, Liu C, Xing Y, Yin H, Ren X, Chen J, Jia D. Sequencing and comparative analysis of chloroplast genomes of three medicinal plants: Gentiana manshurica, G. scabra and G. triflora. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1421-1435. [PMID: 36051231 PMCID: PMC9424396 DOI: 10.1007/s12298-022-01217-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Three species of Gentiana (Gentiana manshurica kitag., Gentiana scabra bunge., and Gentiana triflora pall.) were the main source for an important traditional Chinese medicine, "Longdan", which was first mentioned in " Shennong materia medica Sutra " 2000 years ago. Until recently, there were very few reports on taxonomic classification of these three traditional medicinal Gentiana species. In the current study, chloroplast genomes of the three Gentiana species were sequenced and the phylogenetic analyses were performed in combination with 31 NCBI downloaded Gentiana species sequences and two species of Swertia as outgroup. Based on the phylogenetic results, a new taxonomic classification for Gentiana was proposed, including 4 independent clades with 6 subdivisions (Group 1-Group 6). All the general features, SSR characteristics and gene composition of Gentiana chloroplast genomes strongly supported such a new classification system for Gentiana, which could lay a theoretical foundation for Gentiana in the molecular evolutionary research. Finally, phylogenetic analyisis also demonstrated that the three examined species from Gentiana could cluster together into one group (Group 6), which was far away from the evolutionary position of the medicinal species, Gentiana rigescens Franch, which was consistent with the traditional classification in traditional medicinal uses and taxonomy. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01217-0.
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Affiliation(s)
- Rong Zhao
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
| | - Shuyue Yin
- Beijing Institute of Technology, Beijing, People’s Republic of China
| | - Jianing Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
| | - Chang Liu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
| | - Haibo Yin
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
| | - Xue Ren
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
| | - Jixiang Chen
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
| | - Dingding Jia
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Liaoning Province, Dalian, People’s Republic of China
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13
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Feng Z, Zheng Y, Jiang Y, Miao YJ, Luo GM, Huang L. Complete chloroplast genome of Gentianopsis barbata and comparative analysis with related species from Gentianaceae. Genome 2022; 65:363-375. [DOI: 10.1139/gen-2021-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gentianopsis barbata is an essential medicinal plant in China with high ornamental and medicinal values. Unfortunately, the study of the chloroplast genome of this plant still has a gap. This study sequenced and characterized the complete chloroplast genome of G. barbata. The complete chloroplast genome of G. barbata is a typical circular structure with 151,123 bp. It consists of a large single-copy region (82,690 bp) and a small single-copy region (17,887 bp) separated by a pair of inverted repeats (25,273 bp), which covers 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Repeat analysis showed the highest frequency of palindrome. Thirty-seven simple sequence repeats were identified, most of which were single nucleotides. The bayesian inference tree, maximum likelihood tree, and neighbor joining tree suggested that G. barbata is grouped with Gentianopsis grandis and Gentianopsis paludosa. The divergence time analysis showed that G. barbata diverged at 1.243 Mya. Comparative chloroplast analysis can reveal interspecific diversity, and regions with high variation can be used to develop molecular markers applicable to various research areas. Our results provide new insight into plastome evolution and valuable resource for further studies on G. barbata.
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Affiliation(s)
- Zhan Feng
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, Jiangxi, China
| | - Yan Zheng
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, Jiangxi, China
| | - Yuan Jiang
- Chinese Academy of Medical Sciences & Peking Union Medical College, 12501, Beijing, China
- Dali University, 66359, Dali, China
| | - Yu Jing Miao
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
| | - Guang Ming Luo
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, China
| | - Linfang Huang
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, China
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14
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Cao Q, Gao Q, Ma X, Zhang F, Xing R, Chi X, Chen S. Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau. BMC PLANT BIOLOGY 2022; 22:195. [PMID: 35413790 PMCID: PMC9004202 DOI: 10.1186/s12870-022-03577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/28/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND The genus Swertia is of great medicinal importance and one of the most taxonomically challenging taxa within Gentianaceae, largely due to the morphological similarities of species within this genus and with its closely related genera. Previous molecular studies confirmed its polyphyly but suffered from low phylogenetic resolutions because only limited sequence loci were used. Thus, we conducted the structural, gene evolutionary, and phylogenetic analyses of 11 newly obtained plastomes of Swertia. Our result greatly improved the phylogenetic resolutions in Swertia, shed new light on the plastome evolution and phylogenetic relationships of this genus. RESULTS The 11 Swertia plastomes together with the published seven species proved highly similar in overall size, structure, gene order, and content, but revealed some structural variations caused by the expansion and contraction of the IRb region into the LSC region, due to the heterogeneous length of the ψycf1. The gene rps16 was found to be in a state flux with pseudogenes or completely lost. Similar situation was also documented in other genera of Gentianaceae. This might imply loss of the gene in the common ancestor of Gentianaceae. The distribution plot of ENC vs. GC3 showed all these plastomes arranging very close in the Wright line with an expected ENC value (49-52%), suggesting the codon usage of Swertia was mainly constrained by a GC mutation bias. Most of the genes remained under the purifying selection, however, the cemA was identified under positive selection, possibly reflecting an adaptive response to low CO2 atmospheric conditions during the Late Miocene. Our phylogenomic analyses, based on 74 protein-coding genes (CDS), supported the polyphyly of Swertia with its close allies in the subtribe Swertiinae, presumably due to recent rapid radiation. The topology inferred from our phylogenetic analyses partly supported the current taxonomic treatment. Finally, several highly variable loci were identified, which can be used in future phylogenetic studies and accurate identification of medicinal genuineness of Swertia. CONCLUSIONS Our study confirmed the polyphyly of Swertia and demonstrated the power of plastome phylogenomics in improvement of phylogenetic resolution, thus contributing to a better understanding of the evolutionary history of Swertia.
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Affiliation(s)
- Qian Cao
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingbo Gao
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xiaolei Ma
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Faqi Zhang
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Rui Xing
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Xiaofeng Chi
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Shilong Chen
- Key Laboratory of Crop Molecular Breeding of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
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15
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Zhang Z, Tao M, Shan X, Pan Y, Sun C, Song L, Pei X, Jing Z, Dai Z. Characterization of the complete chloroplast genome of Brassica oleracea var. italica and phylogenetic relationships in Brassicaceae. PLoS One 2022; 17:e0263310. [PMID: 35202392 PMCID: PMC8870505 DOI: 10.1371/journal.pone.0263310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/18/2022] [Indexed: 11/23/2022] Open
Abstract
Broccoli (Brassica oleracea var. italica) is an important B. oleracea cultivar, with high economic and agronomic value. However, comparative genome analyses are still needed to clarify variation among cultivars and phylogenetic relationships within the family Brassicaceae. Herein, the complete chloroplast (cp) genome of broccoli was generated by Illumina sequencing platform to provide basic information for genetic studies and to establish phylogenetic relationships within Brassicaceae. The whole genome was 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The total GC content of the entire chloroplast genome accounts for 36%, while the GC content in each region of SSC,LSC, and IR accounts for 29.1%, 34.15% and 42.35%, respectively. The genome harbored 133 genes, including 88 protein-coding genes, 37 tRNAs, and 8 rRNAs, with 17 duplicates in IRs. The most abundant amino acid was leucine and the least abundant was cysteine. Codon usage analyses revealed a bias for A/T-ending codons. A total of 35 repeat sequences and 92 simple sequence repeats were detected, and the SC-IR boundary regions were variable between the seven cp genomes. A phylogenetic analysis suggested that broccoli is closely related to Brassica oleracea var. italica MH388764.1, Brassica oleracea var. italica MH388765.1, and Brassica oleracea NC_0441167.1. Our results are expected to be useful for further species identification, population genetics analyses, and biological research on broccoli.
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Affiliation(s)
- Zhenchao Zhang
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Meiqi Tao
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Xi Shan
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Yongfei Pan
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Chunqing Sun
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Lixiao Song
- Department of Vegetables, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xuli Pei
- College of Agriculture and Life Science, Kunming University, Kunming, China
| | - Zange Jing
- College of Agriculture and Life Science, Kunming University, Kunming, China
| | - Zhongliang Dai
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
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16
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Sabater B. On the Edge of Dispensability, the Chloroplast ndh Genes. Int J Mol Sci 2021; 22:12505. [PMID: 34830386 PMCID: PMC8621559 DOI: 10.3390/ijms222212505] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/23/2022] Open
Abstract
The polypeptides encoded by the chloroplast ndh genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I. Except for Charophyceae (algae related to higher plants) and a few Prasinophyceae, all eukaryotic algae lack ndh genes. Among vascular plants, the ndh genes are absent in epiphytic and in some species scattered among different genera, families, and orders. The recent identification of many plants lacking plastid ndh genes allows comparison on phylogenetic trees and functional investigations of the ndh genes. The ndh genes protect Angiosperms under various terrestrial stresses, maintaining efficient photosynthesis. On the edge of dispensability, ndh genes provide a test for the natural selection of photosynthesis-related genes in evolution. Variable evolutionary environments place Angiosperms without ndh genes at risk of extinction and, probably, most extant ones may have lost ndh genes recently. Therefore, they are evolutionary endpoints in phylogenetic trees. The low number of sequenced plastid DNA and the long lifespan of some Gymnosperms lacking ndh genes challenge models about the role of ndh genes protecting against stress and promoting leaf senescence. Additional DNA sequencing in Gymnosperms and investigations into the molecular mechanisms of their response to stress will provide a unified model of the evolutionary and functional consequences of the lack of ndh genes.
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Affiliation(s)
- Bartolomé Sabater
- Department of Life Sciences, University of Alcalá, Alcalá de Henares, 28805 Madrid, Spain
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17
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Zhang Y, Yu J, Xia M, Chi X, Khan G, Chen S, Zhang F. Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau. Ecol Evol 2021; 11:16034-16046. [PMID: 34824809 PMCID: PMC8601884 DOI: 10.1002/ece3.8274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/07/2022] Open
Abstract
Genus Comastoma (subt. Swertiinae, Gentianaceae) contains species, such as "Zangyinchen," that are important herbs in Tibetan medicine. The phylogenetic relationship of this within Gentianaceae and the circumscriptions of its species have long been controversial with conflicting morphological and molecular data reported. Here, we used whole chloroplast genome sequences for Comastoma species and related taxa to reconstruct their phylogeny and clarify their taxonomic relationships. The results revealed that the length of all plastome sequenced varied from 149 to 151 kb and have high similarity in structure and gene content. Phylogenomic analysis showed that Comastoma is a monophyletic group, closely related to the genus Lomatogonium. The divergence time estimation showed that Gentianaceae diverged at about 21.81 Ma, while the split of Comastoma occurred at 7.70 Ma. However, the results suggested the crown age of species formation in this genus is after 4.19 Ma. Our results suggest that QTP uplift, the alternation of Quaternary glaciation and interglaciation, and monsoon changes might have acted as drivers of speciation in Comastoma.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mingze Xia
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Gulzar Khan
- Institute for Biology and Environmental SciencesCarl von Ossietzky‐University OldenburgOldenburgGermany
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology & Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
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18
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Li S, Yuan W, He S, Bai W, Wu H. The complete chloroplast genome and phylogenetic analysis of Gentiana arethusae Burkill (Gentianaceae) from China. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:3132-3133. [PMID: 34651079 PMCID: PMC8510589 DOI: 10.1080/23802359.2021.1984334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Gentiana arethusae Burkill is a perennial herb classified in the Gentianaceae. In this study, the complete chloroplast genome of G. arethusae was sequenced and analyzed. The chloroplast genome is 137,458 bp in length and encodes a total of 116 genes, including 71 protein-coding, 37 tRNA, and eight rRNA genes. The genome has a low GC content of 38.0%. Phylogenetic analysis of the genome of G. arethusae resolved it in a clade with Gentiana obconica and Gentiana veitchiorum. The complete chloroplast genome of G. arethusae will be helpful to study the genetic diversity and phylogenetics of the Gentianaceae.
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Affiliation(s)
- Sisi Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wenbin Yuan
- Department of Pratacultural Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shuilian He
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Weiwei Bai
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hongzhi Wu
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
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19
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Ya HY, Miao YW. Complete plastid genome of Gentiana leucomelaena Maxim. (Gentianaceae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2953-2954. [PMID: 34553055 PMCID: PMC8451681 DOI: 10.1080/23802359.2021.1972872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The complete plastid genome of Gentiana leucomelaena Maxim., belonging to the most species-rich section Chondrophyllae in Gentiana, was determined and analyzed in this study. It has a circular-mapping molecular with the length of 131,856 bp, the shortest one among all available Gentiana plastomes. Gentiana leucomelaena has gene mutation, for example ndh and rpl2 intron, and reversed SSC region comparing with the available species in sections Cruciata, Frigida, Kudoa, Isomeria and Microsperma. Phylogenetic analysis showed that G. leucomelaena clustered together with section Cruciata with a long branch. The plastome provides in this work will contribute to elucidate the phylogenetics and evolution in Gentiana.
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Affiliation(s)
- Hui-Yuan Ya
- School of Food and Drug, Luoyang Normal University, Luoyang, People's Republic of China
| | - Yu-Wei Miao
- Construction Management Committee of Xining Garden Expo Park and XiBu Forest Park, Xining, People's Republic of China
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20
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Xu L, Zhou N, Zhao S, Li J, Pei X, Yu J, Guo D. The complete plastid genome of Cotinus coggygria and phylogenetic analysis of the Anacardiaceae. Genet Mol Biol 2021; 44:e20210006. [PMID: 34342605 PMCID: PMC8329748 DOI: 10.1590/1678-4685-gmb-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Cotinus coggygria Scop. (Anacardiaceae) is an important ornamental tree with beautiful characteristics that is grown in China. In this study, the complete plastid genome of C. coggygria was sequenced and assembled. This genome was 158,843 bp in size and presented a typical tetrad structure, consisting of a large single-copy region (87,121 bp), a pair of inverted repeat regions (26,829 bp), and a small single-copy region (18,064 bp). A total of 134 genes were annotated, including 88 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We observed a deletion that caused the loss of the rpl32 gene, and a small expansion of IR regions resulted in the trnH gene accessing IR regions; two copies were obtained. Phylogenetic analysis showed that C. coggygria was most closely related to Pistacia, with 100% bootstrap support within Anacardiaceae. In this study, we report the plastid genome of Cotinus species for the first time, which provides insight into the evolution of the plastid genome in Anacardiaceae and promotes the understanding of Cotinus plants.
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Affiliation(s)
- Lingfeng Xu
- Chongqing Three Gorges University, Chongqing, College of Biology and Food Engineering, Chongqing Engineering Laboratory of Green Planting and Deep Processing of Genuine Medicinal Materials in the Three Gorges Reservoir Region, China
| | - Nong Zhou
- Chongqing Three Gorges University, Chongqing, College of Biology and Food Engineering, Chongqing Engineering Laboratory of Green Planting and Deep Processing of Genuine Medicinal Materials in the Three Gorges Reservoir Region, China
| | - Shunxin Zhao
- Chongqing Three Gorges University, Chongqing, College of Biology and Food Engineering, Chongqing Engineering Laboratory of Green Planting and Deep Processing of Genuine Medicinal Materials in the Three Gorges Reservoir Region, China
| | - Jingling Li
- Southwest University, College of Horticulture and Landscape Architecture, Chongqing, China
| | - Xiaoying Pei
- Southwest University, College of Horticulture and Landscape Architecture, Chongqing, China
| | - Jie Yu
- Southwest University, College of Horticulture and Landscape Architecture, Chongqing, China
| | - Dongqin Guo
- Chongqing Three Gorges University, Chongqing, College of Biology and Food Engineering, Chongqing Engineering Laboratory of Green Planting and Deep Processing of Genuine Medicinal Materials in the Three Gorges Reservoir Region, China
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21
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Fu P, Sun S, Twyford AD, Li B, Zhou R, Chen S, Gao Q, Favre A. Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae). Ecol Evol 2021; 11:3286-3299. [PMID: 33841784 PMCID: PMC8019047 DOI: 10.1002/ece3.7281] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 01/03/2023] Open
Abstract
The structure and sequence of plastid genomes is highly conserved across most land plants, except for a minority of lineages that show gene loss and genome degradation. Understanding the early stages of plastome degradation may provide crucial insights into the repeatability and predictability of genomic evolutionary trends. We investigated these trends in subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled, and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae and all main sections of the species-rich genus Gentiana L. We reconstructed the phylogeny, estimated divergence times, investigated the phylogenetic distribution of putative gene losses, and related these to substitution rate shifts and species' habitats. We obtained a strongly supported topology consistent with earlier studies, with all six genera in Gentianinae recovered as monophyletic and all main sections of Gentiana having full support. While closely related species have very similar plastomes in terms of size and structure, independent gene losses, particularly of the ndh complex, have occurred in multiple clades across the phylogeny. Gene loss was usually associated with a shift in the boundaries of the small single-copy and inverted repeat regions. Substitution rates were variable between clades, with evidence for both elevated and decelerated rate shifts. Independent lineage-specific loss of ndh genes occurred at a wide range of times, from Eocene to Pliocene. Our study illustrates that diverse degradation patterns shape the evolution of the plastid in this species-rich plant group.
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Affiliation(s)
- Peng‐Cheng Fu
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Shan‐Shan Sun
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Alex D. Twyford
- Ashworth LaboratoriesInstitute of Evolutionary BiologyThe University of EdinburghEdinburghUK
- Royal Botanic Garden EdinburghEdinburghUK
| | - Bei‐Bei Li
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Rui‐Qi Zhou
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Shi‐Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
| | - Qing‐Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
| | - Adrien Favre
- Senckenberg Research Institute and Natural History MuseumFrankfurt am MainGermany
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Fu PC, Twyford AD, Sun SS, Wang HY, Xia MZ, Tan CX, Zhou XJ, Chen SL. Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau. AOB PLANTS 2021; 13:plaa068. [PMID: 33510891 PMCID: PMC7821390 DOI: 10.1093/aobpla/plaa068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 05/31/2023]
Abstract
The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centres of diversity for several alpine groups. Although it is known that the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary processes underlying diversity in this genus, especially the formation of narrow endemics, are still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal internal transcribed spacer sequence data. Genetic divergence within G. hoae ~3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Hong-Yu Wang
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Cheng-Xi Tan
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Xiao-Jun Zhou
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
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23
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Zhang X, Sun Y, Landis JB, Lv Z, Shen J, Zhang H, Lin N, Li L, Sun J, Deng T, Sun H, Wang H. Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes. BMC PLANT BIOLOGY 2020; 20:340. [PMID: 32680458 PMCID: PMC7368685 DOI: 10.1186/s12870-020-02518-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied. RESULTS We sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one (atpB) of the three widely used plastid markers (rbcL, atpB and matK) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal protein (RPL and RPS) genes and the RNA polymerase (RPO) genes have higher substitution rates and genetic variations among plastid genes in Gentianeae. Our study revealed that just one (matK) of the three (matK, ndhB and rbcL) widely used markers show high phylogenetic informativeness (PI) value. Due to the high PI and lowest gene-tree discordance, rpoC2 is advocated as a promising plastid DNA barcode for taxonomic studies of Gentianeae. Furthermore, our analyses revealed a positive correlation of evolutionary rates with genetic variation of plastid genes, but a negative correlation with gene-tree discordance under purifying selection. CONCLUSIONS Overall, our results demonstrate the heterogeneity of nucleotide substitution rates and genetic characteristics among plastid genes providing new insights into plastome evolution, while highlighting the necessity of considering gene-tree discordance into phylogenomic studies based on plastome-scale data.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92507, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
| | - Zhenyu Lv
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jun Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiao Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Ya HY, Zhou RQ, Li BB, Fu PC. Complete plastid genome of an alpine plant Gentiana filistyla (Gentianaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1735270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Hui-Yuan Ya
- School of Food and Drug, Luoyang Normal University, Luoyang, China
| | - Rui-Qi Zhou
- School of Life Science, Luoyang Normal University, Luoyang, China
| | - Bei-Bei Li
- School of Life Science, Luoyang Normal University, Luoyang, China
| | - Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, China
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25
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Fu PC, Sun SS, Khan G, Dong XX, Tan JZ, Favre A, Zhang FQ, Chen SL. Population subdivision and hybridization in a species complex of Gentiana in the Qinghai-Tibetan Plateau. ANNALS OF BOTANY 2020; 125:677-690. [PMID: 31922527 PMCID: PMC7103000 DOI: 10.1093/aob/mcaa003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/08/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Hosting several global biodiversity hotspots, the region of the Qinghai-Tibetan Plateau (QTP) is exceptionally species-rich and harbours a remarkable level of endemism. Yet, despite a growing number of studies, factors fostering divergence, speciation and ultimately diversity remain poorly understood for QTP alpine plants. This is particularly the case for the role of hybridization. Here, we explored the evolutionary history of three closely related Gentiana endemic species, and tested whether our results supported the mountain geo-biodiversity hypothesis (MGH). METHODS We genotyped 69 populations across the QTP with one chloroplast marker and 12 nuclear microsatellite loci. We performed phylogeographical analysis, Bayesian clustering, approximate Bayesian computation and principal components analysis to explore their genetic relationship and evolutionary history. In addition, we modelled their distribution under different climates. KEY RESULTS Each species was composed of two geographically distinct clades, corresponding to the south-eastern and north-western parts of their distribution. Thus Gentiana veitchiorum and G. lawrencei var. farreri, which diverged recently, appear to have shared at least refugia in the past, from which their range expanded later on. Indeed, climatic niche modelling showed that both species went through continuous expansion from the Last Interglacial Maximum to the present day. Moreover, we have evidence of hybridization in the northwest clade of G. lawrencei var. farreri, which probably occurred in the refugium located on the plateau platform. Furthermore, phylogenetic and population genetic analyses suggested that G. dolichocalyx should be a geographically limited distinct species with low genetic differentiation from G. lawrencei var. farreri. CONCLUSIONS Climatic fluctuations in the region of the QTP have played an important role in shaping the current genetic structure of G. lawrencei var. farreri and G. veitchiorum. We argue that a species pump effect did occur prior to the Last Interglacial Maximum, thus lending support to the MGH. However, our results do depart from expectations as suggested in the MGH for more recent distribution range and hybridization dynamics.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Strasse, Oldenburg, Germany
| | - Xiao-Xia Dong
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Jin-Zhou Tan
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage, Frankfurt am Main, Germany
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P. R. China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, P. R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P. R. China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, P. R. China
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26
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Conservation and innovation: Plastome evolution during rapid radiation of Rhodiola on the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2019; 144:106713. [PMID: 31863901 DOI: 10.1016/j.ympev.2019.106713] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 01/25/2023]
Abstract
The amount of plastome sequence data available has soared in the last decade, but the nature of plastome evolution during rapid radiations is largely unknown. Moreover, although there is increasing evidence showing that plastomes may have undergone adaptive evolution in order to allow adaptation to various environments, few studies have systematically investigated the role of the plastome in alpine adaptation. To address these questions, we sequenced and analyzed 12 representative species of Rhodiola, a genus which includes ca. 70 perennial herbs mainly growing in alpine habitats in the Qinghai-Tibet Plateau and the Hengduan Mountains. Rapid radiation in this genus was triggered by the uplift of the Qinghai-Tibet Plateau. We also included nine species of Crassulaceae as the outgroups. All plastomes were conserved with respect to size, structure, and gene content and order, with few variations: each contained 134 genes, including 85 protein-coding genes, 37 tRNAs, 8 rRNAs, and 4 potential pseudogenes. Four types of repeat sequence were detected. Slight contraction and expansion of the inverted repeats were also revealed. Both the genome-wide alignment and sequence polymorphism analyses showed that the inverted repeats and coding regions were more conserved than the single-copy regions and the non-coding regions. Positive selection analyses identified three genes containing sites of positive selection (rpl16, ndhA, ndhH), and one gene with a faster than average rate of evolution (psaA). The products of these genes may be involved in the adaptation of Rhodiola to alpine environments such as low CO2 concentration and high-intensity light.
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27
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Sun SS, Zhou XJ, Li ZZ, Song HY, Long ZC, Fu PC. Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae). PeerJ 2019; 7:e8025. [PMID: 31799070 PMCID: PMC6884991 DOI: 10.7717/peerj.8025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 10/11/2019] [Indexed: 11/20/2022] Open
Abstract
Chloroplasts are typically inherited from the female parent and are haploid in most angiosperms, but rare intra-individual heteroplasmy in plastid genomes has been reported in plants. Here, we report an example of plastome heteroplasmy and its characteristics in Gentiana tongolensis (Gentianaceae). The plastid genome of G. tongolensis is 145,757 bp in size and is missing parts of petD gene when compared with other Gentiana species. A total of 112 single nucleotide polymorphisms (SNPs) and 31 indels with frequencies of more than 2% were detected in the plastid genome, and most were located in protein coding regions. Most sites with SNP frequencies of more than 10% were located in six genes in the LSC region. After verification via cloning and Sanger sequencing at three loci, heteroplasmy was identified in different individuals. The cause of heteroplasmy at the nucleotide level in plastome of G. tongolensis is unclear from the present data, although biparental plastid inheritance and transfer of plastid DNA seem to be most likely. This study implies that botanists should reconsider the heredity and evolution of chloroplasts and be cautious with using chloroplasts as genetic markers, especially in Gentiana.
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Affiliation(s)
- Shan-Shan Sun
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
| | - Xiao-Jun Zhou
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hong-Yang Song
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
| | - Zhi-Cheng Long
- HostGene. Co. Ltd., Wuhan, Hubei, People’s Republic of China
| | - Peng-Cheng Fu
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
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28
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Sun S, Wang H, Fu P. Complete plastid genome of Gentiana trichotoma (Gentianaceae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2775-2776. [PMID: 33365723 PMCID: PMC7706570 DOI: 10.1080/23802359.2019.1644231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The complete plastid genome of Gentiana trichotoma was determined and analyzed in this work. It had a circular-mapping molecular with the length of 144,759 bp, has similar gene composition with G. section Cruciata but contains 10 more genes than G. section Kudoa. Phylogenetic analysis showed that G. trichotoma clustered together with section Kudoa rather than section Cruciata. The plastome provided in this work would be useful for elucidation of Gentiana evolution.
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Affiliation(s)
- Shanshan Sun
- School of Life Science, Luoyang Normal University, Luoyang, People's Republic of China
| | - Hui Wang
- School of Life Science, Luoyang Normal University, Luoyang, People's Republic of China
| | - Pengcheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, People's Republic of China
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29
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Fu PC, Ya HY, Liu QW, Cai HM, Chen SL. Out of Refugia: Population Genetic Structure and Evolutionary History of the Alpine Medicinal Plant Gentiana lawrencei var. farreri (Gentianaceae). Front Genet 2018; 9:564. [PMID: 30534138 PMCID: PMC6275180 DOI: 10.3389/fgene.2018.00564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/06/2018] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic structure and evolutionary history of plants contributes to their conservation and utilization and helps to predict their response to environmental changes. The wildflower and traditional Chinese and Tibetan medicinal plant Gentiana lawrencei var. farreri is endemic to the Qinghai-Tibetan Plateau (QTP). To explore its genetic structure and evolutionary history, the genetic diversity, divergence, and demographics were analyzed in individuals from 31 locations across the QTP using 1 chloroplast marker and 10 nuclear microsatellite loci. High genetic diversity was detected in G. lawrencei var. farreri, and most of the genetic variance was found within populations. Values of F ST in G. lawrencei var. farreri from nuclear microsatellite and chloroplast data were 0.1757 and 0.739, respectively. The data indicated the presence of isolation by distance. The southeast edge of the QTP was the main refugium for G. lawrencei var. farreri, and one microrefugium was also detected in the plateau platform of the QTP. Both nuclear microsatellite and chloroplast data indicated that the populations were divided into two geographically structured groups, a southeast group and a northwest group. The current genetic pattern was mainly formed through recolonization from the two independent refugia. Significant melt was detected at the adjacent area of the two geographically structured groups. Approximate Bayesian computation showed that the northwest group had diverged from the southeast group, which then underwent population expansion. Our results suggest that the two-refugia pattern had a significant impact on the genetic structure and evolutionary history of G. lawrencei var. farreri.
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Affiliation(s)
- Peng-Cheng Fu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Hui-Yuan Ya
- College of Food and Drug, Luoyang Normal University, Luoyang, China
| | - Qi-Wei Liu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Hui-Min Cai
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
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30
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Zhang X, Rong C, Qin L, Mo C, Fan L, Yan J, Zhang M. Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships. Molecules 2018; 23:E2917. [PMID: 30413097 PMCID: PMC6278565 DOI: 10.3390/molecules23112917] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 12/29/2022] Open
Abstract
Malus hupehensis belongs to the Malus genus (Rosaceae) and is an indigenous wild crabapple of China. This species has received more and more attention, due to its important medicinal, and excellent ornamental and economical, values. In this study, the whole chloroplast (cp) genome of Malus hupehensis, using a Hiseq X Ten sequencing platform, is reported. The M. hupehensis cp genome is 160,065 bp in size, containing a large single copy region (LSC) of 88,166 bp and a small single copy region (SSC) of 19,193 bp, separated by a pair of inverted repeats (IRs) of 26,353 bp. It contains 112 genes, including 78 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). The overall nucleotide composition is 36.6% CG. A total of 96 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition, a total of 49 long repeats were identified, including 24 forward repeats, 21 palindromic repeats, and four reverse repeats. Comparisons of the IR boundaries of nine Malus complete chloroplast genomes presented slight variations at IR/SC boundaries regions. A phylogenetic analysis, based on 26 chloroplast genomes using the maximum likelihood (ML) method, indicates that M. hupehensis clustered closer ties with M. baccata, M. micromalus, and M. prunifolia than with M. tschonoskii. The availability of the complete chloroplast genome using genomics methods is reported here and provides reliable genetic information for future exploration on the taxonomy and phylogenetic evolution of the Malus and related species.
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Affiliation(s)
- Xin Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chunxiao Rong
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Ling Qin
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chuanyuan Mo
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lu Fan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jie Yan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Manrang Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
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31
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Zhou T, Wang J, Jia Y, Li W, Xu F, Wang X. Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers. Int J Mol Sci 2018; 19:E1962. [PMID: 29976857 PMCID: PMC6073106 DOI: 10.3390/ijms19071962] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 11/30/2022] Open
Abstract
Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (G. dahurica, G. siphonantha and G. officinalis). We further compared them with the previously published plastomes from sect. Cruciata and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (accD, clpP, matK and ycf1) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. Cruciata and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Jian Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Wenli Li
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Fusheng Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
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