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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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Yu X, Qin M, Qu M, Jiang Q, Guo S, Chen Z, Shen Y, Fu G, Fei Z, Huang H, Gao L, Yao X. Genomic analyses reveal dead-end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1528-1543. [PMID: 37258460 DOI: 10.1111/tpj.16336] [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: 03/01/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Despite the importance of hybridization in evolution, the evolutionary consequence of homoploid hybridizations in plants remains poorly understood. Specially, homoploid hybridization events have been rarely documented due to a lack of genomic resources and methodological limitations. Actinidia zhejiangensis was suspected to have arisen from hybridization of Actinidia eriantha and Actinidia hemsleyana or Actinidia rufa. However, this species was very rare in nature and exhibited sympatric distribution with its potential parent species, which implied it might be a spontaneous hybrid of ongoing homoploid hybridization. Here, we illustrate the dead-end homoploid hybridization and genomic basis of isolating barriers between A. eriantha and A. hemsleyana through whole genome sequencing and population genomic analyses. Chromosome-scale genome assemblies of A. zhejiangensis and A. hemsleyana were generated. The chromosomes of A. zhejiangensis are confidently assigned to the two haplomes, and one of them originates from A. eriantha and the other originates from A. hemsleyana. Whole genome resequencing data reveal that A. zhejiangensis are mainly F1 hybrids of A. hemsleyana and A. eriantha and gene flow initiated about 0.98 million years ago, implying both strong genetic barriers and ongoing hybridization between these two deeply divergent kiwifruit species. Five inversions containing genes involved in pollen germination and pollen tube growth might account for the fertility breakdown of hybrids between A. hemsleyana and A. eriantha. Despite its distinct morphological traits and long recurrent hybrid origination, A. zhejiangensis does not initiate speciation. Collectively, our study provides new insights into homoploid hybridization in plants and provides genomic resources for evolutionary and functional genomic studies of kiwifruit.
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Affiliation(s)
- Xiaofen Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Mengyun Qin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghao Qu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sumin Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Zhenghai Chen
- Forest Resources Monitoring Center of Zhejiang Province, Hangzhou, Zhejiang, 310020, China
| | - Yufang Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Guodong Fu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853, USA
| | - Hongwen Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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The comparative studies of complete chloroplast genomes in Actinidia (Actinidiaceae): novel insights into heterogenous variation, clpP gene annotation and phylogenetic relationships. Mol Genet Genomics 2022; 297:535-551. [PMID: 35175427 DOI: 10.1007/s00438-022-01868-4] [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: 07/08/2021] [Accepted: 01/30/2022] [Indexed: 10/19/2022]
Abstract
The genus Actinidia, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species' relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species' phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes' sequences derived from 25 Actinidia taxa. The average genome size is 156,673.38 bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in Actinidia were revealed to be the causal agent leading to the chloroplast genome size expansion. The clpP gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in Actinidia species. Comprehensive sequence analyses indicated the distinct variation at the clpP gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e., rps16 ~ trnQ-UUG, rps4 ~ trnT-UGU, petA ~ psbJ, and rps12 ~ psbB) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying rps12 ~ psbB (including clpP gene and its up/downstream noncoding sequence) were identified as variation hot spots in Actinidia species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25 Actinidia taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in Actinidia. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among Actinidia species.
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Qiu D, Tang P, Yao X. Characterization of the complete chloroplast genome sequence of Actinidia kolomikta. Mitochondrial DNA B Resour 2021; 6:1129-1130. [PMID: 33796764 PMCID: PMC7995872 DOI: 10.1080/23802359.2021.1902408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The whole complete chloroplast (cp) genome sequence of Actinidia kolomikta (formerly A. maloide) was sequenced and assembled from Illumina paired-end sequencing. The cp genome of A. arguta was 157,425 bp long, containing a large single copy region (LSC) of 88,498 bp and a small single copy region (SSC) of 20,475 bp and a pair of inverted repeat regions (IR) of 242,266 bp. It contained 113 different genes, including 79 protein-coding genes, 30 tRNA genes, 4 ribosomal RNA genes. Phylogenetic analysis using concatenated alignments of whole cp genome sequences revealed that A. kolomikta was the sister group to all other groups of Actinidia
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Affiliation(s)
- Dongping Qiu
- College of Forestry Science and Technology, Lishui Vocational and Technical College, Lishui, China
| | - Ping Tang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, China
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, China
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Qi X, Xie X, Zhong C, Li D. The complete chloroplast genome of Actinidia latifolia, a species with high vitamin C content in fruit. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1823260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Xiaoqiong Qi
- Hubei Key Laboratory of Purification and Application of Plant Anti-cancer Active Ingredients, School of Chemistry and Life Science, Hubei University of Education
| | - Xiaodong Xie
- College of Life Sciences, Shanxi Agricultural University, Shanxi, China
| | - Caihong Zhong
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Dawei Li
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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Chen Y, Xu Y, Zhang K, Song Y, He Q, Qian Q, Xu J. The complete chloroplast genome of Actinidia macrosperma. Mitochondrial DNA B Resour 2019; 4:4188-4189. [PMID: 33366376 PMCID: PMC7707781 DOI: 10.1080/23802359.2019.1692733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/09/2019] [Indexed: 11/21/2022] Open
Abstract
Actinidia macrosperma (A. macrosperma) is a medicinal plant in China, which has been well known for its activities against leprosy and cancers. In this study, we assembled and characterized the complete chloroplast (cp) genome sequence of A. macrosperma in an effort to provide genomic resources for promoting its conservation. The cp genome is 156,231 bp in length, containing a pair of 23,720 bp inverted repeat (IR) regions, which is separated by a large single copy region (LSC) of 88,214 bp and a small single copy region (SSC) of 20,577 bp. A total of 132 genes were annotated in this cp genome, including 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis highly supported that A. macrosperma was evolutionarily close to another Actinidia species Actinidia deliciosa.
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Affiliation(s)
- Yi Chen
- Sun Nanjing Automatic Equipments Co. Ltd., Nanjing, China
| | - Yiqing Xu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Kai Zhang
- Nanjing Visiable Information Technology Co. Ltd., Nanjing, China
| | - Yanlin Song
- Shandong Agriculture and Engineering University, Jinan, China
| | - Qiuyu He
- Nanjing XiaoZhuang University, Nanjing, China
| | - Qiuyu Qian
- Nanjing Visiable Information Technology Co. Ltd., Nanjing, China
| | - Jian Xu
- Nanjing Muzhou Software Co. Ltd., Nanjing, China
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Lin H, Jiang L, Zhang F, Bai D. Assembly and phylogenetic analysis of the complete chloroplast genome sequence of Actinidia setosa. Mitochondrial DNA B Resour 2019; 4:3679-3680. [PMID: 33366140 PMCID: PMC7707611 DOI: 10.1080/23802359.2019.1678423] [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: 08/20/2019] [Accepted: 09/25/2019] [Indexed: 11/03/2022] Open
Abstract
The complete chloroplast (cp) genome sequence of Actinidia setosa (A. setosa) was sequenced and assembled into a circular genome of 156,728 bp length using Illumina paired-end data. The cp genome composed of a pair of 24,090 bp inverted repeat (IR) regions separated by a large single copy region (LSC) of 88,256 bp and a small single copy region (SSC) of 20,292 bp. Additionally, a total of 131 genes, including 85 protein-coding genes, 38 tRNA genes and 8 rRNA genes, were identified in the A. setosa cp genome. Phylogenetic analysis showed that A. setosa was evolutionarily close to other two kiwifruits A. deliciosa and A. chinensis.
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Affiliation(s)
- Haifeng Lin
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu, China
- School of Civil Engineering, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ling Jiang
- College of Engineering, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Fuquan Zhang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Di Bai
- College of Engineering, Nanjing Agricultural University, Nanjing, Jiangsu, China
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