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Liu H, Liu X, Sun C, Li HL, Li ZX, Guo Y, Fu XQ, Liao QH, Zhang WL, Liu YQ. Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis 'Hongyang'. Genes (Basel) 2023; 14:2136. [PMID: 38136958 PMCID: PMC10743354 DOI: 10.3390/genes14122136] [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: 10/22/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Actinidia chinensis 'Hongyang', also known as red yangtao (red heart kiwifruit), is a vine fruit tree native to China possessing significant nutritional and economic value. However, information on its genetic diversity and phylogeny is still very limited. The first chloroplast (cp) genome of A. chinensis 'Hongyang' cultivated in China was sequenced using de novo technology in this study. A. chinensis 'Hongyang' possesses a cp genome that spans 156,267 base pairs (bp), exhibiting an overall GC content of 37.20%. There were 132 genes that were annotated, with 85 of them being protein-coding genes, 39 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 49 microsatellite sequences (SSRs) were detected, mainly single nucleotide repeats, mostly consisting of A or T base repeats. Compared with 14 other species, the cp genomes of A. chinensis 'Hongyang' were biased towards the use of codons containing A/U, and the non-protein coding regions in the A. chinensis 'Hongyang' cpDNA showed greater variation than the coding regions. The nucleotide polymorphism analysis (Pi) yielded nine highly variable region hotspots, most in the large single copy (LSC) region. The cp genome boundary analysis revealed a conservative order of gene arrangement in the inverted repeats (IRs) region of the cp genomes of 15 Actinidia plants, with small expansions and contractions of the boundaries. Furthermore, phylogenetic tree indicated that A. chinensis 'Hongyang' was the closest relative to A. indochinensis. This research provides a useful basis for future genetic and evolutionary studies of A. chinensis 'Hongyang', and enriches the biological information of Actinidia species.
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Affiliation(s)
- Han Liu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404000, China
| | - Xia Liu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Chong Sun
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou 434023, China;
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Zhe-Xin Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Yuan Guo
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Xue-Qian Fu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Qin-Hong Liao
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Wen-Lin Zhang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Yi-Qing Liu
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou 434023, China;
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Francisconi AF, Marroquín JAM, Cauz-Santos LA, van den Berg C, Martins KKM, Costa MF, Picanço-Rodrigues D, de Alencar LD, Zanello CA, Colombo CA, Hernández BGD, Amaral DT, Lopes MTG, Veasey EA, Zucchi MI. Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns. Sci Rep 2023; 13:20635. [PMID: 37996522 PMCID: PMC10667357 DOI: 10.1038/s41598-023-44631-4] [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: 01/25/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Jonathan Andre Morales Marroquín
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Luiz Augusto Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina S/N-Novo Horizonte, Feira de SantanaFeira de Santana, Bahia, CEP 44036-900, Brazil
| | - Kauanne Karolline Moreno Martins
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Marcones Ferreira Costa
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
- Universidade Federal do Piauí, BR-343 Km 3.5, Floriano, Piauí, CEP 64808-605, Brazil
| | - Doriane Picanço-Rodrigues
- Departamento de Biologia, Universidade Federal do Amazonas, Avenida Gen. Rodrigo Octávio Jordão Ramos, 3000-Coroado I-Campus Universitário-Senador Arthur Virgílio Filho-Setor Sul, Bloco H, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Luciano Delmodes de Alencar
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Cesar Augusto Zanello
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Carlos Augusto Colombo
- Instituto Agronômico, Av. Theodureto de Almeida Camargo, 1500, Campinas, São Paulo, CEP 13075-630, Brazil
| | | | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo, CEP 09040-040, Brazil
| | - Maria Teresa Gomes Lopes
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Avenida Rodrigo Otávio Ramos, 3000-Bairro Coroado, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11-Bairro São Dimas, Piracicaba, São Paulo, CEP 13418-900, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos Agronegócios (APTA), Polo Centro Sul, Rodovia SP 127 Km 30, CP 28, Piracicaba, São Paulo, CEP 13400-970, Brazil.
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203
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Dong Y, Du C, Yue J, Li W. The complete chloroplast genome and phylogenetic analysis of Acalypha hispida Burm. f. (Euphorbiaceae), an ornamental and medicinal plant. Mitochondrial DNA B Resour 2023; 8:1285-1289. [PMID: 38188445 PMCID: PMC10769557 DOI: 10.1080/23802359.2023.2284414] [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: 09/02/2023] [Accepted: 11/12/2023] [Indexed: 01/09/2024] Open
Abstract
Acalypha hispida Burm. f. (1768) is an evergreen shrub native to New Guinea and the Bismarck Archipelago. Currently, it is widely cultivated as an ornamental and medicinal plant in tropical and subtropical areas worldwide. This study characterized the complete chloroplast genome of A. hispida, which is 172,122 bp in length and consists of large single-copy (LSC) and small single-copy (SSC) regions of 97,025 bp and 19,787 bp, respectively, that are separated by a pair of 27,655 bp inverted repeat (IR) regions. The overall GC content of the genome is 34.22%. The genome contains 131 genes, including 86 protein-coding, 37 tRNA, and eight rRNA genes. Phylogenetic analysis indicates that A. hispida is closely related to Ricinus communis and Cleidiocarpon cavaleriei in the Euphorbiaceae family. The complete chloroplast genome of A. hispida provides genomic resources and potential markers suitable for future species identification and speciation studies of the genus Acalypheae and will also provide important information on the phylogenetic relationships of the Euphorbiaceae family.
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Affiliation(s)
- Yan Dong
- School of Forestry, Xinyang Agriculture and Forestry University, Xinyang, Henan, PR China
- Key Laboratory of Tree Genetics and Breeding of Xinyang, Xinyang, Henan, PR China
| | - Changmei Du
- School of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, Henan, PR China
| | - Jianhua Yue
- School of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, Henan, PR China
| | - Wenyang Li
- School of Forestry, Xinyang Agriculture and Forestry University, Xinyang, Henan, PR China
- Key Laboratory of Tree Genetics and Breeding of Xinyang, Xinyang, Henan, PR China
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204
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Yan R, Gu L, Qu L, Wang X, Hu G. New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes. Int J Mol Sci 2023; 24:16629. [PMID: 38068952 PMCID: PMC10706649 DOI: 10.3390/ijms242316629] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), a small single-copy (SSC) region (18,585-18,768 bp), and a pair of inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of Hydrocotyle plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.
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Affiliation(s)
- Rongrong Yan
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Li Gu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Lu Qu
- Institute of Medicinal Plant Development Yunnan Branch, Chinese Academy of Medical Sciences, Jinghong 666100, China;
| | - Xiaoyu Wang
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Guoxiong Hu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
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205
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Zafar UB, Shahzaib M, Atif RM, Khan SH, Niaz MZ, Shahzad K, Chughtai N, Awan FS, Azhar MT, Rana IA. De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease. Sci Rep 2023; 13:20503. [PMID: 37993468 PMCID: PMC10665356 DOI: 10.1038/s41598-023-45982-8] [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: 05/27/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023] Open
Abstract
Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.
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Affiliation(s)
- Ummul Buneen Zafar
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Shahzaib
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Rana Muhammad Atif
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Muhammad Zeeshan Niaz
- Plant Pathology Research Institute, Ayub Agriculture Research Institute, Faisalabad, 38850, Punjab, Pakistan
| | - Khalid Shahzad
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Nighat Chughtai
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Iqrar Ahmad Rana
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan.
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206
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Li J, Du Y, Xie L, Jin X, Zhang Z, Yang M. Comparative plastome genomics and phylogenetic relationships of the genus Trollius. FRONTIERS IN PLANT SCIENCE 2023; 14:1293091. [PMID: 38046610 PMCID: PMC10690957 DOI: 10.3389/fpls.2023.1293091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Trollius, a genus in the Ranunculaceae family, has significant medicinal and ornamental value. It is widely distributed in China with 16 different species accepted. However, due to the lack of enough samples and information sites, the molecular phylogenetic relationships of Trollius have been unresolved till now. Here we sequenced, assembled and annotated the plastomes of 16 Trollius species to investigate their genomic characteristics, inverted repeat (IR) boundaries, sequence repeats, and hypervariable loci. In addition, the phylogenetic relationships of this genus was reconstructed based on the whole plastomes and the protein-coding sequences data-sets. The plastomes of Trollius ranged between 159,597 bp and 160,202 bp in length, and contained 113 unique genes, including 79 protein coding, 30 tRNA, and 4 rRNA. The IR boundaries were relatively conserved within the genus Trollius. 959 simple sequence repeats and 657 long sequence repeats were detected in the Trollius plastomes. We identified 12 highly polymorphic loci (Pi > 0.0115) that can be used as plastid markers in molecular identification and phylogenetic investigation of the genus. Besides, Trollius was a monophyletic group with the earliest divergence clade being Trollius lilacinus Bunge, and the remaining species were divided into two strongly-supported clades. The phylogeny in our study supported the traditional classification systems based on the color of sepal, but not the previous classification system based on the types and relative lengths of the nectaries, and distribution. The genomic resources provided in our study can be used in the taxonomy of the genus Trollius, promoting the development and utilization of this genus.
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Affiliation(s)
- Jiaxin Li
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Yan Du
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhirong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meiqing Yang
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
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207
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Niu Z, Lin Z, Tong Y, Chen X, Deng Y. Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses. BMC PLANT BIOLOGY 2023; 23:564. [PMID: 37964203 PMCID: PMC10647099 DOI: 10.1186/s12870-023-04532-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Justicia L. is the largest genus in Acanthaceae Juss. and widely distributed in tropical and subtropical regions of the world. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies were mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp.) genomes of 12 Asian plants and combined with the previously published cp. genome of Justicia leptostachya Hemsl. for further comparative genomics and phylogenetic analyses. RESULTS All the cp. genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434-83,676 bp), a small single copy (SSC, 16,833-17,507 bp) and two inverted repeats (IR, 24,947-25,549 bp). GC contents range from 38.1 to 38.4%. All the plastomes contain 114 genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa C. B. Clarke is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for the genus Justicia. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with the morphology evolution. CONCLUSION Our study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.
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Affiliation(s)
- Zhengyang Niu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheli Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, 512005, China
| | - Yi Tong
- School of Chinese Materia Medica Medical, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Liu Z, Huang Y, Chen H, Liu C, Wang M, Bian C, Wang L, Song L. Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat. BMC Genomics 2023; 24:679. [PMID: 37950158 PMCID: PMC10638732 DOI: 10.1186/s12864-023-09760-0] [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: 02/09/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments. RESULTS The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance. CONCLUSIONS In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.
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Affiliation(s)
- Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yuting Huang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
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209
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Liu X, Bai Y, Wang Y, Chen Y, Dong W, Zhang Z. Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae). Int J Mol Sci 2023; 24:16130. [PMID: 38003320 PMCID: PMC10671389 DOI: 10.3390/ijms242216130] [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: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of H. perforatum and compared the genome variation among five Hypericum species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the Hypericum chloroplast genomes. The H. perforatum chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The H. perforatum chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. Hypericum chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five Hypericum species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes-trnK-UUU, infA, and rps16-were lost, and three genes-rps7, rpl23, and rpl32-were pseudogenized in Hypericum. All the Hypericum chloroplast genomes lost the two introns in clpP, the intron in rps12, and the second intron in ycf3. Hypericum chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection.
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Affiliation(s)
- Xinyu Liu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Yuran Bai
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Yachao Wang
- School of Life Sciences, Fudan University, Shanghai 200437, China;
| | - Yifeng Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Zhixiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
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210
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Qiao X, Wang Z, Sun W, Zhu N, Song M. The complete chloroplast genome of Ranunculus ternatus (Ranunculaceae). Mitochondrial DNA B Resour 2023; 8:1209-1214. [PMID: 38239910 PMCID: PMC10796127 DOI: 10.1080/23802359.2023.2278816] [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: 07/27/2023] [Accepted: 10/29/2023] [Indexed: 01/22/2024] Open
Abstract
Ranunculus ternatus Thunb. 1784 is a plant with important medicinal values. Here we report its chloroplast genome. This chloroplast genome was 156,003 bp in length with a GC content of 37.86%. It is composed of a large single copy (LSC) of 85,397 bp and a small single copy (SSC) of 19,856 bp, which are separated by a pair of inverted repeats (IR) of 25,375 bp each. The chloroplast genome contained 110 unique genes, including 77 protein-coding genes, 4 rRNA genes, and 29 tRNA genes. Phylogenetic analysis indicated that R. ternatus was closely related to R. cassubicifolius. This chloroplast genome not only enriches the genome information of Ranunculus but also will be useful for the evolution study of the family Ranunculaceae.
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Affiliation(s)
- Xinrong Qiao
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Zexia Wang
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Wei Sun
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Nailiang Zhu
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Min Song
- College of Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
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211
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Zhu H, Li H. Comprehensive Analysis of the Complete Chloroplast Genome of Cinnamomum daphnoides (Lauraceae), An Endangered Island Endemic Plant. Mol Biotechnol 2023:10.1007/s12033-023-00950-5. [PMID: 37934387 DOI: 10.1007/s12033-023-00950-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023]
Abstract
Cinnamomum daphnoides (Siebold & Zucc 1846) is a rare and endangered island species with a unique Sino-Japanese distribution pattern. However, inormation regarding the species' chloroplast (cp) genome, structural features, and the phylogenetic relationship is still lacking. We utilized high-throughput sequencing technology to assemble and annotate the first cp genome of C. daphnoides (GenBank OR654104), followed by genomic characterization and phylogenetic analysis to fill the gaps in this species' cp genome. Our analysis showed that the cp genome has a quadripartite structure spanning 152,765 bp with a GC content of 39.15%. The genome encodes 126 genes, which include 36 tRNA genes, 8 rRNA genes, and 82 mRNA genes. Specifically, 44 genes are related to photosynthesis, 59 are associated with self-replication, six are other genes, and four have unknown functionality. The Codon usage bias in the genome exhibits a preference for A/U bases. We identified 29 interspaced repeat sequences that belonging to three types of repeat sequences. A total of 217 cpSSR loci were detected with single nucleotide repeats (59.91%) being the most frequent loci, mainly composed of A/T repeats. Our selection pressure analysis revealed that the ycf2 gene experienced strong positive selection (Ka/Ks = 1.81, P > 0.844). Further, we identified three highly variable fragments (psbM, psbT, and ycf1) that can be utilized as specific DNA barcoding markers for species definition and population genetic studies. We conducted boundary analysis, which showed that the structure and gene sequence of the two species were highly conserved. Finally, our phylogenetic analysis supports that C. daphnoides is close to C. cassia in the Cinnamomum genes, indicating that the two species share a common ancestry. Overall, providing genomic information on C. daphnoides will be beneficial for the conservation and utilization of endangered plant genetic resources. It will also serve as a reference for the identification of species and the phylogenetic analysis of Cinnamomum. This information will be useful in future research.
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Affiliation(s)
- Hong Zhu
- Zhejiang Academy of Forestry, Hangzhou, 310023, China.
| | - Hepeng Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
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212
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Xiao Y, Liu J, Wei J, Xiao Z, Li J, Ma Y. Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration. Sci Data 2023; 10:774. [PMID: 37935724 PMCID: PMC10630468 DOI: 10.1038/s41597-023-02699-7] [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: 08/14/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
Sciaenops ocellatus is among the most important artificially introduced farmed fish across 11 countries and regions. However, the frequent occurrence of extreme weather events and breeding escapes have placed great pressure on local marine biodiversity and ecosystems. We reported the de novo assembly and annotation with a contig N50 of 28.30 Mb using PacBio HiFi sequencing and Hi-C technologies, which resulted in a 283-fold increase in contig N50 length and improvement in continuity and quality in complex repetitive region for S. ocellatus compared to the previous version. In total, 257.36 Mb of repetitive sequences accounted for 35.48% of the genome, and 22,845 protein-coding genes associated with a BUSCO value of 98.32%, were identified by genome annotation. Moreover, 54 hub genes rapidly responding to hypoosmotic stress were identified by WGCNA. The high-quality chromosome-scale S. ocellatus genome and candidate resistance-related gene sets will not only provide a genomic basis for genetic improvement via molecular breeding, but will also lay an important foundation for investigating the molecular regulation of rapid responses to stress.
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Affiliation(s)
- Yongshuang Xiao
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jing Liu
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Jiehong Wei
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhizhong Xiao
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jun Li
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Yuting Ma
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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213
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Lu G, Wang W, Mao J, Li Q, Que Y. Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications. BMC PLANT BIOLOGY 2023; 23:541. [PMID: 37924024 PMCID: PMC10625231 DOI: 10.1186/s12870-023-04529-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Mitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported. RESULTS This study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019 bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (≥ 50 bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437 bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523 bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3). CONCLUSIONS This study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.
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Affiliation(s)
- Guilong Lu
- College of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Wenhua Wang
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China
| | - Juan Mao
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China
| | - Qing Li
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China.
| | - Youxiong Que
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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214
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Jiang M, Ni Y, Zhang J, Li J, Liu C. Complete mitochondrial genome of Mentha spicata L. reveals multiple chromosomal configurations and RNA editing events. Int J Biol Macromol 2023; 251:126257. [PMID: 37573900 DOI: 10.1016/j.ijbiomac.2023.126257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
Mentha spicata L. is a valuable plant that yields spearmint oil, widely utilized in the pharmaceutical, chemical, and cosmetic industries. The mitochondrial genome (mitogenome) is an essential material for molecular breeding and evolution studies. Here, the mitogenome of M. spicata was assembled by combining Nanopore and Illumina reads. It consisted of a linear chromosome (Ch1) and two circular chromosomes (Ch2 and Ch3). Furthermore, we showed two pairs of repeats (R1 and R2) mediated recombinations resulting in multiple chromosomal configurations. The R1-mediated-recombination generated a large molecule formed by joining Ch2 and Ch1. Similarly, the R2-mediated-recombination generated a large molecule formed by joining Ch3 and Ch1. Then, we identified 17 mitochondrial plastid DNAs (MTPTs) by comparing the mitogenome and cpgenome. The MTPT14 was conserved in multiple species, which has undergone the same evolutionary process as the two organellar genomes among M. spicata, Hesperelaea palmeri and Castilleja paramensis. Based on the RNA-seq reads, 246 RNA editing sites were predicted, resulting in the conversion of cytosine to uracil bases. Furthermore, we successfully validated 40 out of 43 predicted sites. This project reported a complex structure of the M. spicata mitogenome resulting from repeat-mediated recombinations, which will provide valuable information for gene function study and the breeding of different varieties.
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Affiliation(s)
- Mei Jiang
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Yang Ni
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China
| | - Jianjie Zhang
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, PR China
| | - Jingling Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China.
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215
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Ye H, Fan J, Hou Y, Yue H, Ruan R, Li S, Hu C, Xie Y, Li C. Chromosome-level genome assembly of the largefin longbarbel catfish ( Hemibagrus macropterus). Front Genet 2023; 14:1297119. [PMID: 38028621 PMCID: PMC10646426 DOI: 10.3389/fgene.2023.1297119] [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: 09/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The largefin longbarbel catfish, Hemibagrus macropterus, is an economically important fish species in southwestern China, with males growing faster than females. This study presents a high-quality chromosome-level genome assembly of the largefin longbarbel catfish, generated by integrating Illumina short reads, PacBio HiFi long reads, and Hi-C data. The assembled genome size was 858.5 Mb, with a contig and scaffold N50 of 5.8 Mb and 28.4 Mb, respectively. A total of 656 contigs were successfully anchored to 30 pseudochromosomes with a BUSCO score of 97.7%, consistent with the number of chromosomes analyzed by karyotype. The genome contained 29.5% repeat sequences, and a predicted total of 26,613 protein-coding genes, of which 25,769 (96.8%) were functionally annotated in different databases. Evolutionary analysis showed that H. macropterus was most closely related to H. wyckioides, with a divergence time of approximately 16.3 million years. Chromosomal syntenic relationships among H. macropterus, H. wyckioides, and Pelteobagrus fulvidraco revealed a one-to-one relationship for most chromosomes, except for break, fission, and inversion of some chromosomes. The first high-quality reference genome will not only provide a valuable genetic resource for the study of sex determination mechanisms and genetic breeding of largefin longbarbel catfish, but also contribute to comparative analyses of genome and chromosome evolution within Siluriformes.
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Affiliation(s)
- Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jiahui Fan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yanling Hou
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Rui Ruan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Shuang Li
- Chongqing Fishery Sciences Research Institute, Chongqing, China
| | - Chongjiang Hu
- Chongqing Fishery Sciences Research Institute, Chongqing, China
| | - Yong Xie
- Chongqing Fishery Sciences Research Institute, Chongqing, China
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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216
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Bei L, He C, Liu J, Han C, Zhou H, Zhaorigetu, Siqintuya, Li J, Su X, Wang Y, Chen Q, Nashun, Daolema, Meng H. Genome-wide identification and characterization of microsatellite markers in Bactrian Camel. Genomics 2023; 115:110726. [PMID: 37832857 DOI: 10.1016/j.ygeno.2023.110726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
Simple sequence repeats (SSRs) have been widely used for parentage testing, marker-assisted selection, and evolutionary studies. The insufficient availability of SSR markers in Bactrian camels partially accounts for the lack of systematic breeding. Therefore, we aimed to establish a comprehensive SSR dataset for the Bactrian camel. Our approach involved genome searching to locate every SSR in the genome, SSR-enriched sequencing to acquire polymorphism information, and literature research to collect published data. The resulting dataset contains 213,711 SSRs and details their characteristics, including genome coordinates, motifs, lengths, annotations, PCR primers, and polymorphism information. The dataset reveals a biased distribution of SSRs in the Bactrian camel genome, reflecting the mutation mechanism and complex evolution of SSRs. In practice, we successfully demonstrated the utility of the dataset through parentage testing using 15 randomly selected SSRs. This comprehensive dataset can facilitate systematic breeding and enable QTL mapping and GWAS of the Bactrian camel.
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Affiliation(s)
- Lanxin Bei
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Chuan He
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Jiajia Liu
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Chengxiao Han
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Hao Zhou
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Zhaorigetu
- Animal Husbandry Institute of Alxa League, 750306, Inner Mongolia, China
| | - Siqintuya
- Animal Husbandry Institute of Alxa League, 750306, Inner Mongolia, China
| | - Jing Li
- Animal Husbandry Institute of Alxa League, 750306, Inner Mongolia, China
| | - Xue Su
- Animal Husbandry Institute of Alxa League, 750306, Inner Mongolia, China
| | - Yunfei Wang
- Bayannur Institute of Agriculture & Animal Husbandry Science, 015000, Inner Mongolia, China
| | - Qiujv Chen
- Bayannur Institute of Agriculture & Animal Husbandry Science, 015000, Inner Mongolia, China
| | - Nashun
- Alxa Left Banner Agriculture and Animal Husbandry Comprehensive Administrative Law Enforcement Brigade, 735499, Inner Mongolia, China
| | - Daolema
- Animal Husbandry Institute of Alxa League, 750306, Inner Mongolia, China.
| | - He Meng
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240 Shanghai, China.
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217
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Sun M, Cheng Y, Gao C, Peng H, Wang N, Gu W, Lu D. Construction and characterization of microsatellite markers for the Schistosoma japonicum isolate from a hilly area of China based on whole genome sequencing. Parasitol Res 2023; 122:2737-2748. [PMID: 37710024 DOI: 10.1007/s00436-023-07976-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/10/2023] [Indexed: 09/16/2023]
Abstract
Schistosoma japonicum had once caused the greatest disease burden in China and has still been transmitted in some hilly areas, for example, in Shitai of Anhui province, where rodents are projected to be the main reservoir. This may lead to a critical need of molecular tools with high efficiency in monitoring the dynamic of the rodent-associated S. japonicum, as an appropriate amount of schistosome input can re-establish its life cycle in a place with snails and then result in the re-emergence of schistosomiasis. Therefore, the goal of this study was to develop high polymorphic microsatellites from the whole genome of rodent-associated S. japonicum strain to monitor its transmission dynamic. We sampled the hilly schistosome isolate from Shitai of Anhui in China and sequenced the parasite with the next-generation sequencing technology. The whole genome was assembled with four different approaches. We then developed 71 microsatellite markers at a genome-wide scale throughout two best assembled genomes. Based on their chromosome mapping and the expected length of targeted sequences, we selected 24 markers for the development of multiplex reactions. Two multiplexes composed of 10 loci were finally developed, and their potential was revealed by their successful application on and capturing the genetic diversity of three schistosome populations. The selected 10 markers, each with clear chromosome location and characteristics, will be greatly useful in tracing the dispersal pathways or/and dynamics of the rodent-associated S. japonicum or others in the hilly area of China or elsewhere.
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Affiliation(s)
- Mengtao Sun
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Yuheng Cheng
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Changzhe Gao
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Hanqi Peng
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Ning Wang
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Weiling Gu
- Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, China.
| | - Dabing Lu
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China.
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Shan T, Xu J, Zhong X, Zhang J, He B, Tao Y, Wu J. Full-length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba. PHYSIOLOGIA PLANTARUM 2023; 175:e14104. [PMID: 38148235 DOI: 10.1111/ppl.14104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/28/2023]
Abstract
Glechoma longituba has been frequently used in treating urolithiasis and cholelithiasis due to the presence of flavonoids, which are its major bioactive constituents. However, research on the molecular background of flavonoid biosynthesis in G. longituba is limited. In this study, we used single-molecule real-time combined with next-generation sequencing technologies to construct the complete transcriptome of G. longituba. We identified 404,648 non-redundant transcripts, including 249,697 coding sequences, 197,811 simple sequence repeats, 174,846 long noncoding RNA, and 176,554 coding RNA. Moreover, we functionally annotated 346,218 isoforms (85.56%) and identified 86,528 differentially expressed genes. We also identified 55 non-redundant full-length isoforms related to the flavonoid biosynthetic pathway. Pearson correlation analysis revealed that the expression levels of some key genes of the flavonoid biosynthesis pathway were significantly positively correlated with the flavonoid metabolites. Furthermore, we performed bioinformatics analysis (sequence and structural) of isoform_47029 (encoding flavanone 3-hydroxylase) and isoform_53692 (encoding flavonol synthase) to evaluate their potential biological functions. Finally, we validated gene expression levels of 12 flavonoid-related key enzyme genes using quantitative real-time PCR. Overall, this study provides full-length transcriptome information on G. longituba for the first time and valuable molecular resources for further research on the medicinal properties of this plant.
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Affiliation(s)
- Tingyu Shan
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jingyao Xu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Xinxin Zhong
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jingjing Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Bing He
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
| | - Yijia Tao
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, China
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Guo H, Liu Q, Chen Y, Niu H, Zhao Q, Song H, Pang R, Huang X, Zhang J, Zhao Z, Liu D, Zhu J. Comprehensive assembly and comparative examination of the full mitochondrial genome in Castanea mollissima Blume. Genomics 2023; 115:110740. [PMID: 37923179 DOI: 10.1016/j.ygeno.2023.110740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The Chinese chestnut, Castanea mollissima Blume, a nut-bearing tree native to China and North Korea, belongs to the Fagaceae family. As an important genetic resource, C. mollissima is vital in enhancing edible chestnut varieties and offers significant insights into the origin and evolution of chestnut species. While the chloroplast genome of C. mollissima has been sequenced, its mitochondrial genome (mitogenome) remains largely uncharted. In this study, we have characterized the C. mollissima mitogenome, assembling it utilizing reads from both BGI and Nanopore sequencing platforms, and conducted a comparative analysis with the mitochondrial genomes of closely related species. The mitogenome of C. mollissima manifests a polycyclic structure consisting of two circular molecules measuring 363,232 bp and 24,806 bp, respectively. This genome encompasses 35 unique protein-coding genes, 19 tRNA genes, and three rRNA genes. A total of 139 SSRs were identified throughout the entire C. mollissima mitogenome. Furthermore, the combined length of homologous fragments between the chloroplast and mitochondrial genomes was 5766 bp, constituting 1.49% of the mitogenome. We also predicted 484 RNA editing sites in C. mollissima, demonstrating C-to-U RNA editing. Phylogenetic analysis of related species' mitogenomes showed that C. mollissima was closely related to Lithocarpus litseifolius (Hance) Chun and Quercus acutissima Carruth. Interestingly, the mitogenome sequences of C. mollissima, L. litseifolius, Q. acutissima, Fagus sylvatica L., and Juglans mandshurica Maxim did not show conservation in their alignments, indicating frequent genome reorganization. This report marks the inaugural study of the C. mollissima mitogenome, serving as a benchmark genome for economically significant plants within the Castanea genus. Moreover, it supplies invaluable information that can guide future molecular breeding efforts and contribute to the broader understanding of chestnut genomics.
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Affiliation(s)
- Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Qiong Liu
- Shandong Refining and Chemical Energy Group Co., Ltd., Jinan 250199, China
| | - Ying Chen
- Shandong Provincial Forestry Protection and Development Service Center, Jinan 250109, China
| | - Hongyun Niu
- Shandong Provincial Center of Aviation Emergency and Rescue, Jinan 250014, China
| | | | - Hui Song
- Shandong Institute of Land Spatial Data and Remote Sensing Technology, Jinan 250002, China
| | - Ruidong Pang
- Shandong Provincial Archives of Natural Resources, Jinan 250013, China
| | - Xiaolu Huang
- Guangxi Forestry Research Institute, Nanning 530002, China
| | - Jingzheng Zhang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Zhiheng Zhao
- Guangxi Forestry Research Institute, Nanning 530002, China; Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China.
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China.
| | - Jingle Zhu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China.
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Chen X, Li B, Zhang X. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Sci Rep 2023; 13:18731. [PMID: 37907468 PMCID: PMC10618267 DOI: 10.1038/s41598-023-45421-8] [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: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
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Affiliation(s)
- Xiaoli Chen
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Buyu Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
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Akash M, Shiyab S, Saleh M, Hasan SM, AbuHussein M, Al-Awaida W. Development and Validation of Gene-Based SSR Markers in the Genus Mesembryanthemum. SCIENTIFICA 2023; 2023:6624354. [PMID: 37937238 PMCID: PMC10627716 DOI: 10.1155/2023/6624354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/26/2023] [Accepted: 10/14/2023] [Indexed: 11/09/2023]
Abstract
Bioinformatics tools have been employed for the direct development of gene-based simple sequence repeat (SSR) markers. Through the analysis of 28,056 Mesembryanthemum expressed sequence tag (EST) sequences, a total of 5,851 ESTs containing SSRs were identified, amounting to approximately 17.07 Mb. Among these, 938 EST sequences harbored more than one SSR marker, and 788 EST-SSR sequences were found in compound form. The most prevalent types of SSR motifs were mononucleotide repeats (MNRs), accounting for 44%, followed by di-nucleotide repeats (DNRs) at 37%, and trinucleotide repeats (TNRs) at 16%. Notably, TNR or longer SSR motifs primarily consisted of shorter repeat lengths, with only 51 motifs containing 10 or more repeats. The BLASTX analysis successfully assigned functions to 4,623 (79%) of the EST sequences. Among the developed primer sets, 21 primers amplified a total of 65 alleles, with primer PMA79 EST-SSR exhibiting the maximum of six alleles. The polymorphic information content (PIC) values ranged from 0 to 0.76, with a mean of 0.47. The marker index (MI) and discriminating power (D) values reached 0.66 (primer PMA63) and 0.95 (primer PMA20), respectively. Utilizing the unweighted pair group method with arithmetic mean (UPGMA), a dendrogram was constructed, successfully segregating the 24 Mesembryanthemum genotypes into three distinct clusters, with a similarity coefficient ranging from 0.96 to 0.38. In this study, we have developed a total of 83 EST-SSR primer pairs specific to the Mesembryanthemum genus. These newly developed EST-SSRs will serve as valuable tools for researchers, particularly molecular breeders, enabling gene-based identification and trait selection through marker-assisted breeding approaches.
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Affiliation(s)
- Muhanad Akash
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, Jordan
| | - Safwan Shiyab
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, Jordan
| | - Mohammed Saleh
- Department of Nutrition and Food Technology, School of Agriculture, The University of Jordan, Amman 11942, Jordan
| | - Shireen M. Hasan
- Hamdi Mango Center for Scientific Research (HMCSR), The University of Jordan, Amman, Jordan
| | | | - Wajdy Al-Awaida
- Department of Biology and Biotechnology, American University of Madaba, Madaba, Jordan
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Xiong C, Huang Y, Li Z, Wu L, Liu Z, Zhu W, Li J, Xu R, Hong X. Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China. BMC Genomics 2023; 24:648. [PMID: 37891463 PMCID: PMC10612195 DOI: 10.1186/s12864-023-09563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/08/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND The Begonia species are common shade plants that are mostly found in southwest China. They have not been well studied despite their medicinal and decorative uses because gene penetration, decreased adaptability, and restricted availability are all caused by frequent interspecific hybridization. RESULT To understand the patterns of mutation in the chloroplast genomes of different species of Begonia, as well as their evolutionary relationships, we collected seven Begonia species in China and sequenced their chloroplast genomes. Begonia species exhibit a quadripartite structure of chloroplast genomes (157,634 - 169,694 bp), consisting of two pairs of inverted repeats (IR: 26,529 - 37,674 bp), a large single copy (LSC: 75,477 - 86,500 bp), and a small single copy (SSC: 17,861 - 18,367 bp). 128-143 genes (comprising 82-93 protein-coding genes, 8 ribosomal RNAs, and 36-43 transfer RNAs) are found in the chloroplast genomes. Based on comparative analyses, this taxon has a relatively similar genome structure. A total of six substantially divergent DNA regions (trnT-UGU-trnL-UAA, atpF-atpH, ycf4-cemA, psbC-trnS-UGA, rpl32-trnL-UAG, and ccsA-ndhD) are found in the seventeen chloroplast genomes. These regions are suitable for species identification and phylogeographic analysis. Phylogenetic analysis shows that Begonia species that were suited to comparable environments grouped in a small clade and that all Begonia species formed one big clade in the phylogenetic tree, supporting the genus' monophyly. In addition, positive selection sites were discovered in eight genes (rpoC1, rpoB, psbE, psbK, petA, rps12, rpl2, and rpl22), the majority of which are involved in protein production and photosynthesis. CONCLUSION Using these genome resources, we can resolve deep-level phylogenetic relationships between Begonia species and their families, leading to a better understanding of evolutionary processes. In addition to enhancing species identification and phylogenetic resolution, these results demonstrate the utility of complete chloroplast genomes in phylogenetically and taxonomically challenging plant groupings.
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Affiliation(s)
- Chao Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China
| | - Yang Huang
- College of Tourism and Landscape Architecture, Guilin University of Technology, Guilin, Guangxi, 541006, People's Republic of China
| | - Zhenglong Li
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, 230601, People's Republic of China
| | - Lan Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Zhiguo Liu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China
| | - Wenjun Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China
| | - Jianhui Li
- College of Chemistry and Material Engineering, Quzhou University, Quzhou, Zhejiang, 324000, People's Republic of China
| | - Ran Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, People's Republic of China.
| | - Xin Hong
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, 230601, People's Republic of China.
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Yang T, Aishan S, Zhu J, Qin Y, Liu J, Liu H, Tie J, Wang J, Qin R. Chloroplast Genomes and Phylogenetic Analysis of Three Carthamus (Asteraceae) Species. Int J Mol Sci 2023; 24:15634. [PMID: 37958617 PMCID: PMC10648744 DOI: 10.3390/ijms242115634] [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: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The genus Carthamus Linnaeus, which belongs to the tribe Cardueae in the Asteraceae family, originated in the Mediterranean region and consists of approximately 20 species worldwide. Understanding the phylogeny of the Carthamus is crucial for the cultivation of C. tinctorius. Although chloroplast genomes are widely used for species identification and evolutionary studies, there have been limited investigations on the chloroplast genomes of Carthamus species. In this study, we assembled the chloroplast genomes of C. persicus, C. tinctorius × C. persicus, and C. lanatus and combined them with the five chloroplast genomes of C. tinctorius for comparative genomic analysis. The sizes of the chloroplast genomes of C. lanatus, C. persicus, and C. tinctorius × C. persicus were 152,602 bp, 153,177 bp, and 153,177 bp, respectively. Comparative analysis showed that the chloroplast genome structures of the four Carthamus species were highly conserved. Additionally, the phylogenomic analysis demonstrated that the plastid genome and angiosperms353 dataset significantly improved the phylogenetic support of Carthamus species. This analysis supported Carthamus as a monophyletic taxon and its internal division into the sect. Carthamus and sect. Atractylis. The Carthamus was closely related to Carduncellus, Femeniasia, Phonus, and Centaurea. In conclusion, this study not only expands our understanding of the cp genomes of Carthamus species but also provides support for more comprehensive phylogenetic studies of Carthamus.
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Affiliation(s)
- Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
| | - Saimire Aishan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
| | - Jiale Zhu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
| | - Yonghua Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
| | - Jun Tie
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
- College of Computer Science, South-Central Minzu University, Wuhan 430074, China
| | - Jiangqing Wang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
- College of Computer Science, South-Central Minzu University, Wuhan 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.)
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Zhang F, Kang H, Gao L. Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species, Oryza granulata and Comparative Mitochondrial Genomic Analyses of the Genus Oryza. Life (Basel) 2023; 13:2114. [PMID: 38004254 PMCID: PMC10672236 DOI: 10.3390/life13112114] [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: 09/23/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
Wild upland rice species, including Oryza granulata, possess unique characteristics that distinguish them from other Oryza species. For instance, O. granulata characteristically has a GG genome and is accordingly classified as a basal lineage of the genus Oryza. Here, we deployed a versatile hybrid approach by integrating Illumina and PacBio sequencing data to generate a high-quality mitochondrial genome (mitogenome) assembly for O. granulata. The mitogenome of O. granulata was 509,311 base pairs (bp) with sixty-seven genes comprising two circular chromosomes, five ribosomal RNA (rRNA) coding genes, twenty-five transfer RNA (tRNA) coding genes, and thirty-seven genes coding for proteins. We identified a total of 378 simple sequence repeats (SSRs). The genome also contained 643 pairs of dispersed repeats comprising 340 palindromic and 303 forward. In the O. granulata mitogenome, the length of 57 homologous fragments in the chloroplast genome occupied 5.96% of the mitogenome length. Collinearity analysis of three Oryza mitogenomes revealed high structural variability and frequent rearrangements. Phylogenetic analysis showed that, compared to other related genera, O. granulata had the closest genetic relationship with mitogenomes reported for all members of Oryza, and occupies a position at the base of the Oryza phylogeny. Comparative analysis of complete mitochondrial genome assemblies for Oryza species revealed high levels of mitogenomic diversity, providing a foundation for future conservation and utilization of wild rice biodiversity.
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Affiliation(s)
- Fen Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Haiqi Kang
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
| | - Lizhi Gao
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
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Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
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Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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226
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Su H, Ding X, Liao B, Zhang D, Huang J, Bai J, Xu S, Zhang J, Xu W, Qiu X, Gong L, Huang Z. Comparative chloroplast genomes provided insights into the evolution and species identification on the Datureae plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1270052. [PMID: 37941675 PMCID: PMC10628451 DOI: 10.3389/fpls.2023.1270052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Generally, chloroplast genomes of angiosperms are always highly conserved but carry a certain number of variation among species. In this study, chloroplast genomes of 13 species from Datureae tribe that are of importance both in ornamental gardening and medicinal usage were studied. In addition, seven chloroplast genomes from Datureae together with two from Solanaceae species retrieved from the National Center for Biotechnology Information (NCBI) were integrated into this study. The chloroplast genomes ranged in size from 154,686 to 155,979 and from 155,497 to 155,919 bp for species of Datura and Brugmansia, respectively. As to Datura and Brugmansia, a total of 128 and 132 genes were identified, in which 83 and 87 protein coding genes were identified, respectively; Furthermore, 37 tRNA genes and 8 rRNA genes were both identified in Datura and Brugmansia. Repeats analysis indicated that the number and type varied among species for Simple sequence repeat (SSR), long repeats, and tandem repeats ranged in number from 53 to 59, 98 to 99, and 22 to 30, respectively. Phylogenetic analysis based on the plastid genomes supported the monophyletic relationship among Datura and Brugmansia and Trompettia, and a refined phylogenic relationships among each individual was resolved. In addition, a species-specific marker was designed based on variation spot that resulted from a comparative analysis of chloroplast genomes and verified as effective maker for identification of D. stramonium and D. stramonium var. inermis. Interestingly, we found that 31 genes were likely to be under positive selection, including genes encoding ATP protein subunits, photosystem protein subunit, ribosome protein subunits, NAD(P)H dehydrogenase complex subunits, and clpP, petB, rbcL, rpoCl, ycf4, and cemA genes. These genes may function as key roles in the adaption to diverse environment during evolution. The diversification of Datureae members was dated back to the late Oligocene periods. These chloroplast genomes are useful genetic resources for taxonomy, phylogeny, and evolution for Datureae.
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Affiliation(s)
- He Su
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaoxia Ding
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Baosheng Liao
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danchun Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juan Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Junqi Bai
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Subing Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jing Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Wen Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaohui Qiu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Lu Gong
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Zhihai Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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Mehmetoğlu E, Kaymaz Y, Ateş D, Kahraman A, Tanyolaç MB. The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species. Sci Rep 2023; 13:17871. [PMID: 37857674 PMCID: PMC10587350 DOI: 10.1038/s41598-023-44599-1] [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: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The Cicer reticulatum is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of C. reticulatum consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of C. reticulatum was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between C. reticulatum and C. arietinum. Phylogenetic analysis further indicated that the closest evolutionary relative to C. arietinum was C. reticulatum, whereas the previously sequenced wild Cicer species displayed slight distinctions across their entire coding regions. Several genomic regions, such as clpP and ycf1, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the Cicer genus. The first complete cp genome sequence of C. reticulatum will provide novel insights for future genetic research on Cicer crops.
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Affiliation(s)
- Ezgi Mehmetoğlu
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Yasin Kaymaz
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Duygu Ateş
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Abdullah Kahraman
- Faculty of Agriculture, Department of Field Crops, Harran University, S. Urfa, 64000, Şanlıurfa, Turkey
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Li H, Song K, Li B, Zhang X, Wang D, Dong S, Yang L. CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis. Int J Mol Sci 2023; 24:15317. [PMID: 37894996 PMCID: PMC10607008 DOI: 10.3390/ijms242015317] [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: 08/31/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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229
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Inglis PW, Cavalcanti TB, Facco MG, Bakker FT, Graham SA. A comprehensive genus-level phylogeny and biogeographical history of the Lythraceae based on whole plastome sequences. ANNALS OF BOTANY 2023; 132:293-318. [PMID: 37439499 PMCID: PMC10583215 DOI: 10.1093/aob/mcad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND AND AIMS The Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide. METHODS Plastomes of representative species of 18 distinct Lythraceae genera were sequenced and annotated. Together with existing sequences, plastomes of all 28 currently accepted genera in the Lythraceae were brought together for the first time. The plastomes were aligned and a Bayesian phylogenetic hypothesis was produced. We then conducted a time-calibrated Bayesian analysis and a biogeographical analysis. KEY RESULTS Plastome-based Bayesian and maximum-likelihood phylogenetic trees are generally congruent with recent nuclear phylogenomic data and resolve two deeply branching major clades in the Lythraceae. One major clade concentrates shrubby and arboreal South American and African genera that inhabit seasonally dry environments, with larger, often winged seeds, adapted to dispersal by the wind. The second major clade concentrates North American, Asian, African and several near-cosmopolitan herbaceous, shrubby and arboreal genera, often inhabiting humid or aquatic environments, with smaller seeds possessing structures that facilitate dispersal by water. CONCLUSIONS We hypothesize that the Lythraceae dispersed early in the Late Cretaceous from South American to North American continents, with subsequent expansion in the Late Cretaceous of a North American lineage through Laurasia to Africa via a boreotropical route. Two later expansions of South American clades to Africa in the Palaeocene and Eocene, respectively, are also hypothesized. Transoceanic dispersal in the family is possibly facilitated by adaptations to aquatic environments that are common to many extant genera of the Lythraceae, where long-distance dispersal and vicariance may be invoked to explain several remarkable disjunct distributions in Lythraceae clades.
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Affiliation(s)
- Peter W Inglis
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Av. W5 Norte (final), Caixa Postal 02372 – Brasília, DF – CEP 70770-917, Brazil
| | - Taciana B Cavalcanti
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Av. W5 Norte (final), Caixa Postal 02372 – Brasília, DF – CEP 70770-917, Brazil
| | - Marlon G Facco
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Postbus 647, NL-6700 AP, Wageningen, The Netherlands
| | - Shirley A Graham
- Missouri Botanical Garden, 4344 Shaw Boulevard, Saint Louis, MO 63110, USA
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230
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Tu XD, Zhao Z, Zhou CY, Zeng MY, Gao XY, Li MH, Liu ZJ, Chen SP. Comparative Analysis of Plastomes in Elsholtzieae: Phylogenetic Relationships and Potential Molecular Markers. Int J Mol Sci 2023; 24:15263. [PMID: 37894943 PMCID: PMC10607353 DOI: 10.3390/ijms242015263] [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: 09/19/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The Elsholtzieae, comprising ca. 7 genera and 70 species, is a small tribe of Lamiaceae (mint family). Members of Elsholtzieae are of high medicinal, aromatic, culinary, and ornamentals value. Despite the rich diversity and value of Elsholtzieae, few molecular markers or plastomes are available for phylogenetics. In the present study, we employed high-throughput sequencing to assemble two Mosla plastomes, M. dianthera and M. scabra, for the first time, and compared with other plastomes of Elsholtzieae. The plastomes of Elsholtzieae exhibited a quadripartite structure, ranging in size from 148,288 bp to 152,602 bp. Excepting the absence of the pseudogene rps19 in Elsholtzia densa, the exhaustive tally revealed the presence of 132 genes (113 unique genes). Among these, 85 protein-coding genes (CDS), 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1) were annotated. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. Notably, the E. eriostchya plastid genome exhibited increased GC content regions in the LSC and SSC, resulting in an increased overall GC content of the entire plastid genome. The E. densa plastid genome displayed modified boundaries due to inverted repeat (IR) contraction. The sequences of CDS and intergenic regions (IGS) with elevated variability were identified as potential molecular markers for taxonomic inquiries within Elsholtzieae. Phylogenetic analysis indicated that four genera formed monophyletic entities, with Mosla and Perilla forming a sister clade. This clade was, in turn, sister to Collinsonia, collectively forming a sister group to Elsholtzia. Both CDS, and CDS + IGS could construct a phylogenetic tree with stronger support. These findings facilitate species identification and DNA barcoding investigations in Elsholtzieae and provide a foundation for further exploration and resource utilization within this tribe.
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Affiliation(s)
- Xiong-De Tu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cheng-Yuan Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xu-Yong Gao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi-Pin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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231
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Zhao H, Wang W, Yang Y, Wang Z, Sun J, Yuan K, Rabbi SMHA, Khanam M, Kabir MS, Seraj ZI, Rahman MS, Zhang Z. A high-quality chromosome-level wild rice genome of Oryza coarctata. Sci Data 2023; 10:701. [PMID: 37838726 PMCID: PMC10576809 DOI: 10.1038/s41597-023-02594-1] [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: 06/12/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
Oryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O. coarctata. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb and an N50 of 23.1 Mb, which were assembled into scaffolds with Hi-C data, anchoring 96.99% of the assembly onto 24 chromosomes. The genome assembly comprises 45,571 genes, and repetitive content contributes 25.5% of the genome. This study provides the novel identification of the KK and LL genome types of the genus Oryza, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of O. coarctata is a valuable resource for rice research and molecular breeding.
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Affiliation(s)
- Hang Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Wenzheng Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yirong Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiwei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaijun Yuan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Duke university, Durham, USA
| | | | - Munnujan Khanam
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | | | - Zeba I Seraj
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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232
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Ning HJ, Gui FF, Tian EW, Yang LY. The novel developed microsatellite markers revealed potential hybridization among Cymbidium species and the interspecies sub-division of C. goeringii and C. ensifolium. BMC PLANT BIOLOGY 2023; 23:492. [PMID: 37833649 PMCID: PMC10571305 DOI: 10.1186/s12870-023-04499-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Orchids (Cymbidium spp.) exhibit significant variations in floral morphology, pollinator relations, and ecological habitats. Due to their exceptional economic and ornamental value, Cymbidium spp. have been commercially cultivated for centuries. SSR markers are extensively used genetic tools for biology identification and population genetics analysis. RESULT In this study, nine polymorphic EST-SSR loci were isolated from Cymbidium goeringii using RNA-Seq technology. All nine SSR loci showed transferability in seven other congeneric species, including 51 cultivars. The novel SSR markers detected inter-species gene flow among the Cymbidium species and intra-species sub-division of C. goeringii and C. ensifolium, as revealed by neighborhood-joining and Structure clustering analyses. CONCLUSION In this study, we developed nine microsatellites using RNA-Seq technology. These SSR markers aided in detecting potential gene flow among Cymbidium species and identified the intra-species sub-division of C. goeringii and C. ensifolium.
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Affiliation(s)
- Hui-Juan Ning
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Fang-Fang Gui
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - En-Wei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
| | - Li-Yuan Yang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou, 311300, Zhejiang, China.
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233
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Zhou Q, Ni Y, Li J, Huang L, Li H, Chen H, Liu C. Multiple configurations of the plastid and mitochondrial genomes of Caragana spinosa. PLANTA 2023; 258:98. [PMID: 37831319 DOI: 10.1007/s00425-023-04245-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
MAIN CONCLUSION In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes. Caragana spinosa belongs to the Papilionoidea subfamily and has significant pharmaceutical value. To explore the possible interaction between the organelle genomes, we assembled and analyzed the plastome and mitogenome of C. spinosa using the Illumina and Nanopore DNA sequencing data. The plastome of C. spinosa was 129,995 bp belonging to the inverted repeat lacking clade (IRLC), which contained 77 protein-coding genes, 29 tRNA genes, and four rRNA genes. The mitogenome was 378,373 bp long and encoded 54 unique genes, including 33 protein-coding, three ribosomal RNA (rRNA), and 18 transfer RNA (tRNA) genes. In addition to the single circular conformation, alternative conformations mediated by one and four repetitive sequences in the plastome and mitogenome were identified and validated, respectively. The inverted repeat (PDR12, the 12th dispersed repeat sequence in C. spinosa plastome) of plastome mediating recombinant was conserved in the genus Caragana. Furthermore, we identified 14 homologous fragments by comparing the sequences of mitogenome and plastome, including eight complete tRNA genes. A phylogenetic analysis of protein-coding genes extracted from the plastid and mitochondrial genomes revealed congruent topologies. Analyses of sequence divergence found one intergenic region, trnN-GUU-ycf1, exhibiting a high degree of variation, which can be used to develop novel molecular markers to distinguish the nine Caragana species accurately. This plastome and mitogenome of C. spinosa could provide critical information for the molecular breeding of C. spinosa and be used as a reference genome for other species of Caragana. In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes.
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Affiliation(s)
- Qingqing Zhou
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Yang Ni
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Jingling Li
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Linfang Huang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Husheng Li
- Shenzhou Space Biotechnology Group, Beijing, 100190, People's Republic of China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
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234
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Lin X, Lee SY, Ni J, Zhang X, Hu X, Zou P, Wang W, Liu G. Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in Bougainvillea. Int J Mol Sci 2023; 24:15138. [PMID: 37894819 PMCID: PMC10607086 DOI: 10.3390/ijms242015138] [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: 09/04/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Bougainvillea is popular in ornamental horticulture for its colorful bracts and excellent adaptability, but the complex genetic relationship among this genus is fuzzy due to limited genomic data. To reveal more genomic resources of Bougainvillea, we sequenced and assembled the complete chloroplast (cp) genome sequences of Bougainvillea spectabilis 'Splendens'. The cp genome size was 154,869 bp in length, containing 86 protein-coding genes, 38 tRNAs, and eight rRNAs. Cp genome comparison across 12 Bougainvillea species (B. spectabilis, B. glabra, B. peruviana, B. arborea, B. praecox, B. stipitata, B. campanulata, B. berberidifolia, B. infesta, B. modesta, B. spinosa, and B. pachyphylla) revealed five mutational hotspots. Phylogenetic analysis suggested that B. spectabilis published previously and B. glabra clustered into one subclade as two distinct groups, sister to the subclade of B. spectabilis 'Splendens'. We considered the phylogeny relationships between B. spectabilis and B. glabra to be controversial. Based on two hypervariable regions and three common plastid regions, we developed five molecular markers for species identification in Bougainvillea and applied them to classify 53 ornamental Bougainvillea cultivars. This study provides a valuable genetic resource for Bougainvillea breeding and offers effective molecular markers to distinguish the representative ornamental species of Bougainvillea.
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Affiliation(s)
- Xinggu Lin
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai 71800, Malaysia;
| | - Jianzhong Ni
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Xiaomin Zhang
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- College of Forestry, Hainan University, Haikou 570228, China
| | - Xing Hu
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Peishan Zou
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Faculty of Health and Life Sciences, INTI International University, Nilai 71800, Malaysia;
| | - Wei Wang
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
| | - Guofeng Liu
- Guangzhou Landscape Plant Germplasm Resource Nursery, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China; (X.L.); (J.N.); (X.Z.); (X.H.); (P.Z.); (W.W.)
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510540, China
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Ni Y, Zhang X, Li J, Lu Q, Chen H, Ma B, Liu C. Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1261012. [PMID: 37885664 PMCID: PMC10598636 DOI: 10.3389/fpls.2023.1261012] [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: 07/18/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Background Coffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica's nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. Results We sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution. Conclusion Our study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.
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Affiliation(s)
| | | | | | | | | | | | - Chang Liu
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 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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Yu J, Han Y, Xu H, Han S, Li X, Niu Y, Chen S, Zhang F. Structural divergence and phylogenetic relationships of Ajania (Asteraceae) from plastomes and ETS. BMC Genomics 2023; 24:602. [PMID: 37817095 PMCID: PMC10566131 DOI: 10.1186/s12864-023-09716-4] [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: 04/13/2023] [Accepted: 10/04/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Ajania Poljakov, an Asteraceae family member, grows mostly in Asia's arid and semi-desert areas and is a significant commercial and decorative plant. Nevertheless, the genus' classification has been disputed, and the evolutionary connections within the genus have not been thoroughly defined. Hence, we sequenced and analyzed Ajania's plastid genomes and combined them with ETS data to assess their phylogenetic relationships. RESULTS We obtained a total of six new Ajania plastid genomes and nine ETS sequences. The whole plastome lengths of the six species sampled ranged from 151,002 bp to 151,115 bp, showing conserved structures. Combined with publicly available data from GenBank, we constructed six datasets to reconstruct the phylogenetic relationships, detecting nucleoplasmic clashes. Our results reveal the affinities of Artemisia, Chrysanthemum and Stilpnolepis to Ajania and validate the early taxonomy reclassification. Some of the plastid genes with low phylogenetic information and gene trees with topological differences may have contributed to the ambiguous phylogenetic results of Ajania. There is extensive evolutionary rate heterogeneity in plastid genes. The psbH and ycf2 genes, which are involved in photosynthesis and ATP transport, are under selective pressure. Plastomes from Ajania species diverged, and structural aspects of plastomes may indicate some of the real evolutionary connections. We suggest the ycf1 gene as a viable plastid DNA barcode because it has significant nucleotide diversity and better reflects evolutionary connections. CONCLUSION Our findings validate the early Ajania taxonomy reclassification and show evolutionary rate heterogeneity, genetic variety, and phylogenetic heterogeneity of plastid genes. This research might provide new insights into the taxonomy and evolution of Ajania, as well as provide useful information for germplasm innovation and genetic enhancement in horticultural species.
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Affiliation(s)
- Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yun Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Shuang Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiaoping Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yu Niu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China.
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, 810008, China.
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238
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Li DM, Liu HL, Pan YG, Yu B, Huang D, Zhu GF. Comparative Chloroplast Genomics of 21 Species in Zingiberales with Implications for Their Phylogenetic Relationships and Molecular Dating. Int J Mol Sci 2023; 24:15031. [PMID: 37834481 PMCID: PMC10648771 DOI: 10.3390/ijms241915031] [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: 09/10/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Zingiberales includes eight families and more than 2600 species, with many species having important economic and ecological value. However, the backbone phylogenetic relationships of Zingiberales still remain controversial, as demonstrated in previous studies, and molecular dating based on chloroplast genomes has not been comprehensively studied for the whole order. Herein, 22 complete chloroplast genomes from 21 species in Zingiberales were sequenced, assembled, and analyzed. These 22 genomes displayed typical quadripartite structures, which ranged from 161,303 bp to 163,979 bp in length and contained 111-112 different genes. The genome structures, gene contents, simple sequence repeats, long repeats, and codon usage were highly conserved, with slight differences among these genomes. Further comparative analysis of the 111 complete chloroplast genomes of Zingiberales, including 22 newly sequenced ones and the remaining ones from the national center for biotechnology information (NCBI) database, identified three highly divergent regions comprising ccsA, psaC, and psaC-ndhE. Maximum likelihood and Bayesian inference phylogenetic analyses based on chloroplast genome sequences found identical topological structures and identified a strongly supported backbone of phylogenetic relationships. Cannaceae was sister to Marantaceae, forming a clade that was collectively sister to the clade of (Costaceae, Zingiberaceae) with strong support (bootstrap (BS) = 100%, and posterior probability (PP) = 0.99-1.0); Heliconiaceae was sister to the clade of (Lowiaceae, Strelitziaceae), then collectively sister to Musaceae with strong support (BS = 94-100%, and PP = 0.93-1.0); the clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)) was sister to the clade of (Musaceae, (Heliconiaceae, (Lowiaceae, Strelitziaceae))) with robust support (BS = 100%, and PP = 1.0). The results of divergence time estimation of Zingiberales indicated that the crown node of Zingiberales occurred approximately 85.0 Mya (95% highest posterior density (HPD) = 81.6-89.3 million years ago (Mya)), with major family-level lineages becoming from 46.8 to 80.5 Mya. These findings proved that chloroplast genomes could contribute to the study of phylogenetic relationships and molecular dating in Zingiberales, as well as provide potential molecular markers for further taxonomic and phylogenetic studies of Zingiberales.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (H.-L.L.); (Y.-G.P.); (B.Y.); (D.H.)
| | | | | | | | | | - Gen-Fa Zhu
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (H.-L.L.); (Y.-G.P.); (B.Y.); (D.H.)
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Choi K, Hwang Y, Hong JK, Kang JS. Comparative Plastid Genome and Phylogenomic Analyses of Potamogeton Species. Genes (Basel) 2023; 14:1914. [PMID: 37895263 PMCID: PMC10606940 DOI: 10.3390/genes14101914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Potamogetonaceae are aquatic plants divided into six genera. The largest genus in the family is Potamogeton, which is morphologically diverse with many hybrids and polyploids. Potamogetonaceae plastomes were conserved in genome size (155,863 bp-156,669 bp), gene contents (113 genes in total, comprising 79 protein-coding genes and 30 tRNA and 4 rRNA genes), and GC content (36.5%). However, we detected a duplication of the trnH gene in the IR region of the Potamogeton crispus and P. maakianus plastomes. A comparative analysis of Alismatales indicated that the plastomes of Potamogetonaceae, Cymodaceae, and Ruppiaceae have experienced a 6-kb inversion of the rbcL-trnV region and the ndh complex has been lost in the Najas flexilis plastome. Five divergent hotspots (rps16-trnQ, atpF intron, rpoB-trnC, trnC-psbM, and ndhF-rpl32) were identified among the Potamogeton plastomes, which will be useful for species identification. Phylogenetic analyses showed that the family Potamogetonaceae is a well-defined with 100% bootstrap support and divided into two different clades, Potamogeton and Stuckenia. Compared to the nucleotide substitution rates among Alismatales, we found neutral selection in all plastid genes of Potamogeton species. Our results reveal the complete plastome sequences of Potamogeton species, and will be helpful for taxonomic identification, the elucidation of phylogenetic relationships, and the plastome structural analysis of aquatic plants.
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Affiliation(s)
- KyoungSu Choi
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (Y.H.); (J.-K.H.)
| | - Yong Hwang
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (Y.H.); (J.-K.H.)
| | - Jeong-Ki Hong
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (Y.H.); (J.-K.H.)
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea;
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240
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Yisilam G, Liu Z, Turdi R, Chu Z, Luo W, Tian X. Assembly and comparative analysis of the complete mitochondrial genome of Isopyrum anemonoides (Ranunculaceae). PLoS One 2023; 18:e0286628. [PMID: 37796878 PMCID: PMC10553351 DOI: 10.1371/journal.pone.0286628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/19/2023] [Indexed: 10/07/2023] Open
Abstract
Ranunculaceae is a large family of angiosperms comprising 2500 known species-a few with medicinal and ornamental values. Despite this, only two mitochondrial genomes (mitogenomes) of the family have been released in GenBank. Isopyrum anemonoides is a medicinal plant belonging to the family Ranunculaceae, and its chloroplast genome has recently been reported; however, its mitogenome remains unexplored. In this study, we assembled and analyzed the complete mitochondrial genome of I. anemonoides and performed a comparative analysis against different Ranunculaceae species, reconstructing the phylogenetic framework of Isopyrum. The circular mitogenome of I. anemonoides has a length of 206,722 bp, with a nucleotide composition of A (26.4%), T (26.4%), C (23.6%), and G (23.6%), and contains 62 genes, comprising 37 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Abundantly interspersed repetitive and simple sequence repeat (SSR) loci were detected in the I. anemonoides mitogenome, with tetranucleotide repeats accounting for the highest proportion of SSRs. By detecting gene migration, we observed gene exchange between the chloroplast and mitogenome in I. anemonoides, including six intact tRNA genes, six PCG fragments, and fragments from two rRNA genes. Comparative mitogenome analysis of three Ranunculaceae species indicated that the PCG contents were conserved and the GC contents were similar. Selective pressure analysis revealed that only two genes (nad1 and rpl5) were under positive selection during their evolution in Ranunculales, and two specific RNA editing sites (atp6 and mttB) were detected in the I. anemonoides mitogenome. Moreover, a phylogenetic analysis based on the mitogenomes of I. anemonoides and the other 15 taxa accurately reflected the evolutionary and taxonomic status of I. anemonoides. Overall, this study provides new insights into the genetics, systematics, and evolution of mitochondrial evolution in Ranunculaceae, particularly I. anemonoides.
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Affiliation(s)
- Gulbar Yisilam
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Zhiyou Liu
- City Management and Service Centre of Tiemenguan, Xinjiang, China
| | - Rayhangul Turdi
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Zhenzhou Chu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Wei Luo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Xinmin Tian
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Guangxi Normal University, Ministry of Education, Guilin, 541004, China
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241
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Islam MS, Chekhovskiy K, Saha MC. Dig up tall fescue plastid genomes for the identification of morphotype-specific DNA variants. BMC Genomics 2023; 24:586. [PMID: 37789301 PMCID: PMC10546690 DOI: 10.1186/s12864-023-09631-8] [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: 05/10/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species. Hexaploid tall fescue has three distinct morphotypes used either as forage or turf purposes. Its chloroplast genome is conserved due to it being maternally inherited to the next generation progenies. To identify morphotype-specific DNA markers and the genetic variations, plastid genomes of all three tall fescue morphotypes, i.e., Continental cv. Texoma MaxQ II, Rhizomatous cv. Torpedo, and Mediterranean cv. Resolute, have been sequenced using Illumina MiSeq sequencing platform. RESULTS The plastid genomes of Continental-, Rhizomatous-, and Mediterranean tall fescue were assembled into circular master molecules of 135,283 bp, 135,336 bp, and 135,324 bp, respectively. The tall fescue plastid genome of all morphotypes contained 77 protein-coding, 20 tRNAs, four rRNAs, two pseudo protein-coding, and three hypothetical protein-coding genes. We identified 630 SNPs and 124 InDels between Continental and Mediterranean, 62 SNPs and 20 InDels between Continental and Rhizomatous, and 635 SNPs and 123 InDels between Rhizomatous and Mediterranean tall fescue. Only four InDels in four genes (ccsA, rps18, accD, and ndhH-p) were identified, which discriminated Continental and Rhizomatous plastid genomes from the Mediterranean plastid genome. Here, we identified and reported eight InDel markers (NRITCHL18, NRITCHL35, NRITCHL43, NRITCHL65, NRITCHL72, NRITCHL101, NRITCHL104, and NRITCHL110) from the intergenic regions that can successfully discriminate tall fescue morphotypes. Divergence time estimation revealed that Mediterranean tall fescue evolved approximately 7.09 Mya, whereas the divergence between Continental- and Rhizomatous tall fescue occurred about 0.6 Mya. CONCLUSIONS To our knowledge, this is the first report of the assembled plastid genomes of Rhizomatous and Mediterranean tall fescue. Our results will help to identify tall fescue morphotypes at the time of pre-breeding and will contribute to the development of lawn and forage types of commercial varieties.
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Affiliation(s)
- Md Shofiqul Islam
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
- Genetics Laboratory, Indiana Crop Improvement Association, 7700 Stockwell Road, Lafayette, IN, 47909, USA.
- Department of Agronomy, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47906, USA.
| | - Konstantin Chekhovskiy
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Malay C Saha
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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242
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Yan M, Dong S, Gong Q, Xu Q, Ge Y. Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny. Sci Rep 2023; 13:16495. [PMID: 37779129 PMCID: PMC10543443 DOI: 10.1038/s41598-023-43638-1] [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: 02/28/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.
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Affiliation(s)
- Meixiu Yan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qiuyi Gong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qin Xu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
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243
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Song N, Ma S, Zhao X, Zhao J, Zhao L. Genomic Characteristics of Okamejei kenojei and the Implications to Its Evolutionary Biology Study. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:815-823. [PMID: 37651024 DOI: 10.1007/s10126-023-10242-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
Okamejei kenojei is an important economic species widely distributed in shallow coastal waters of the western North Pacific. In this study, the whole-genome survey analysis of O. kenojei was conducted to reveal its genomic characteristics. The genome size was estimated to be 2027.44 Mb, the repeat sequence content was 44.90%, and the heterozygous ratio was 1.04%. The mitochondrial genome excavated from the sequencing data was 16,974 bp, and it can form the closed circular molecule. The phylogenetic tree based on 13 protein-coding gene sequences supported the validity of Okamejei and assisted the conclusion that Raja porosa was the junior synonym of O. kenojei. Plenty of potential microsatellite loci were identified, and the distribution frequency was estimated to be approximately 236.3 SSRs per Mb. Among all motif types of microsatellites, the dinucleotide repeats were dominant (82.59%), followed by the trinucleotide repeats (8.05%), tetranucleotide repeats (5.80%), pentanucleotide repeats (2.83%), and hexanucleotide repeats (0.72%). The results of the present study could not only provide useful information for understanding the genome structure and functional characteristics of O. kenojei, but also lay the foundation for the subsequent mapping of the whole genome.
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Affiliation(s)
- Na Song
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Siyu Ma
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Xiang Zhao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Jiabao Zhao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Linlin Zhao
- Ministry of Natural Resources, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Qingdao, 266061, Shandong, China.
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Rasoarahona R, Wattanadilokchatkun P, Panthum T, Jaisamut K, Lisachov A, Thong T, Singchat W, Ahmad SF, Han K, Kraichak E, Muangmai N, Koga A, Duengkae P, Antunes A, Srikulnath K. MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes. Chromosome Res 2023; 31:29. [PMID: 37775555 DOI: 10.1007/s10577-023-09738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/11/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.
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Affiliation(s)
- Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kitipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixes, Av. General Norton de Matos, S/N, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, S/N, 4169-007, Porto, Portugal
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok, 10900, Thailand.
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand.
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Yang T, Wu Z, Tie J, Qin R, Wang J, Liu H. A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus Chrysosplenium. Int J Mol Sci 2023; 24:14735. [PMID: 37834185 PMCID: PMC10572340 DOI: 10.3390/ijms241914735] [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: 08/23/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Chrysosplenium, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of Alternifolia and Oppositifolia based on phyllotaxy. Although there has been some progress in the phylogeny of Chrysosplenium over the years, the phylogenetic position of some species is still controversial. In this study, we assembled chloroplast genomes (cp genomes) of 34 Chrysosplenium species and performed comparative genomic and phylogenetic analyses in combination with other cp genomes of previously known Chrysosplenium species, for a total of 44 Chrysosplenium species. The comparative analyses revealed that cp genomes of Chrysosplenium species were more conserved in terms of genome structure, gene content and arrangement, SSRs, and codon preference, but differ in genome size and SC/IR boundaries. Phylogenetic analysis showed that cp genomes effectively improved the phylogenetic support and resolution of Chrysosplenium species and strongly supported Chrysosplenium species as a monophyletic taxon and divided into three branches. The results also showed that the sections of Alternifolia and Oppositifolia were not monophyletic with each other, and that C. microspermum was not clustered with other Chrysosplenium species with alternate leaves, but with C. sedakowii into separate branches. In addition, we identified 10 mutational hotspot regions that could serve as potential DNA barcodes for Chrysosplenium species identification. In contrast to Peltoboykinia, the clpP and ycf2 genes of Chrysosplenium were subjected to positive selection and had multiple significant positive selection sites. We further detected a significant positive selection site on the petG gene between the two sections of Chrysosplenium. These evolutionary characteristics may be related to the growth environment of Chrysosplenium species. This study enriches the cp genomes of Chrysosplenium species and provides a reference for future studies on its evolution and origin.
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Affiliation(s)
- Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China;
| | - Jun Tie
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
- College of Computer Science, South-Central Minzu University, Wuhan 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
| | - Jiangqing Wang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
- College of Computer Science, South-Central Minzu University, Wuhan 430074, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
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Anwar G, Mamut R, Wang J. Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species. J Fungi (Basel) 2023; 9:969. [PMID: 37888225 PMCID: PMC10607270 DOI: 10.3390/jof9100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 10/28/2023] Open
Abstract
In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (PCGs), 2 rRNAs, 26-27 tRNAs and an unidentified open reading frame (ORF). The PCG length, AT skew and GC skew varied among the 15 PCGs in the five mitogenomes. Among the 15 PCGs, cox2 had the least K2P genetic distance, indicating that the gene was highly conserved. The synteny analysis revealed that the coding regions were highly conserved in the Peltigera mitochondrial genomes, but gene rearrangement occurred in the intergenic regions. The phylogenetic analysis based on the 14 PCGs showed that the 11 Peltigera species formed well-supported topologies, indicating that the protein-coding genes in the mitochondrial genome may be used as a reliable molecular tool in the study of the phylogenetic relationship of Peltigera.
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Affiliation(s)
| | - Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830017, China; (G.A.); (J.W.)
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Yan R, Geng Y, Jia Y, Xiang C, Zhou X, Hu G. Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1265641. [PMID: 37828930 PMCID: PMC10565954 DOI: 10.3389/fpls.2023.1265641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023]
Abstract
Introduction The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. Methods In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. Results The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Discussion Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.
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Affiliation(s)
- Rongrong Yan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yanfei Geng
- College of Tea Science, Guizhou University, Guiyang, Guizhou, China
| | - Yuhuan Jia
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Chunlei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xinxin Zhou
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Guoxiong Hu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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248
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Corvalán LCJ, Sobreiro MB, Carvalho LR, Dias RO, Braga-Ferreira RS, Targueta CP, Silva-Neto CME, Berton BW, Pereira AMS, Diniz-filho JAF, Telles MPC, Nunes R. Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1258794. [PMID: 37822334 PMCID: PMC10562606 DOI: 10.3389/fpls.2023.1258794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
Abstract
Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.
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Affiliation(s)
| | - Mariane B. Sobreiro
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Larissa R. Carvalho
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Renata O. Dias
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Ramilla S. Braga-Ferreira
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, Rondonópolis, Brazil
| | - Cintia P. Targueta
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | | | | | | | - José A. F. Diniz-filho
- Laboratório de Ecologia Teórica e Síntese, Universidade Federal de Goiás, Goiânia, Brazil
| | - Mariana P. C. Telles
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto Federal de Goiás, Goiás, Brazil
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Zhou CY, Zeng MY, Gao X, Zhao Z, Li R, Wu Y, Liu ZJ, Zhang D, Li MH. Characteristics and Comparative Analysis of Seven Complete Plastomes of Trichoglottis s.l. (Aeridinae, Orchidaceae). Int J Mol Sci 2023; 24:14544. [PMID: 37833995 PMCID: PMC10572978 DOI: 10.3390/ijms241914544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Trichoglottis exhibits a range of rich variations in colors and shapes of flower and is a valuable ornamental orchid genus. The genus Trichoglottis has been expanded by the inclusion of Staurochilus, but this Trichoglottis sensu lato (s.l.) was recovered as a non-monophyletic genus based on molecular sequences from one or a few DNA regions. Here, we present phylogenomic data sets, incorporating complete plastome sequences from seven species (including five species sequenced in this study) of Trichoglottis s.l. (including two species formerly treated as Staurochilus), to compare plastome structure and to reconstruct the phylogenetic relationships of this genus. The seven plastomes possessed the typical quadripartite structure of angiosperms and ranged from 149,402 bp to 149,841 bp with a GC content of 36.6-36.7%. These plastomes contain 120 genes, which comprise 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, all ndh genes were pseudogenized or lost. A total of 98 (T. philippinensis) to 134 (T. ionosma) SSRs and 33 (T. subviolacea) to 46 (T. ionosma) long repeats were detected. The consistent and robust phylogenetic relationships of Trichoglottis were established using a total of 25 plastid genomes from the Aeridinae subtribe. The genus Trichoglottis s.l. was strongly supported as a monophyletic group, and two species formerly treated as Staurochilus were revealed as successively basal lineages. In addition, five mutational hotspots (trnNGUU-rpl32, trnLUAA, trnSGCU-trnGUCC, rbcL-accD, and trnTGGU-psbD) were identified based on the ranking of PI values. Our research indicates that plastome data is a valuable source for molecular identification and evolutionary studies of Trichoglottis and its related genera.
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Affiliation(s)
- Cheng-Yuan Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Xuyong Gao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Ruyi Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Yuhan Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (M.-Y.Z.); (X.G.); (Z.Z.); (R.L.); (Y.W.); (Z.-J.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Zhao Z, Zeng MY, Wu YW, Li JW, Zhou Z, Liu ZJ, Li MH. Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species. Int J Mol Sci 2023; 24:14437. [PMID: 37833887 PMCID: PMC10572996 DOI: 10.3390/ijms241914437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78-82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25-38 long repeats and 130-149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA-petN, trnDGUC-trnYGUA, trnSGCU-trnGUCC, and rpl32-trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.
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Affiliation(s)
- Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Yu-Wei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Jin-Wei Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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