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Li B, Muhammad N, Zhang S, Lan Y, Yang Y, Han S, Liu M, Yang M. Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources. PLANTS (BASEL, SWITZERLAND) 2023; 12:2885. [PMID: 37571038 PMCID: PMC10421302 DOI: 10.3390/plants12152885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
Jujube (Ziziphus jujuba Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.
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Affiliation(s)
- Bin Li
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Noor Muhammad
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shufeng Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yunxin Lan
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yihan Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shoukun Han
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Meng Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
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Xiang N, Lu B, Yuan T, Yang T, Guo J, Wu Z, Liu H, Liu X, Qin R. De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum. Genes (Basel) 2023; 14:genes14020279. [PMID: 36833206 PMCID: PMC9956384 DOI: 10.3390/genes14020279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Affiliation(s)
- Niyan Xiang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- 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
| | - Bojie Lu
- 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
| | - Tao Yuan
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - 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
| | - Jiani Guo
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, 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
| | - Xing Liu
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (X.L.); (R.Q.)
| | - 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
- Correspondence: (X.L.); (R.Q.)
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Guo R, Zhang YH, Zhang HJ, Landis JB, Zhang X, Wang HC, Yao XH. Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot. BMC PLANT BIOLOGY 2022; 22:89. [PMID: 35227218 PMCID: PMC8883688 DOI: 10.1186/s12870-022-03464-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic-continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic-continental gradient and 'oceanic' adaptation. RESULTS The phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic-continental gradient of the species and fit the 'refugia in refugia' pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to 'oceanic' adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods. CONCLUSIONS Overall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic-continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to 'oceanic' adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.
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Affiliation(s)
- Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Yong-Hua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Hua-Jie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiao-Hong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Parmar R, Seth R, Sharma RK. Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze). Sci Rep 2022; 12:201. [PMID: 34996959 PMCID: PMC8742041 DOI: 10.1038/s41598-021-03848-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
Tea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory “Transcription factor (TF) genes” can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (Chr) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.
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Affiliation(s)
- Rajni Parmar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India.
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Yue J, Liu J, Tang W, Wu YQ, Tang X, Li W, Yang Y, Wang L, Huang S, Fang C, Zhao K, Fei Z, Liu Y, Zheng Y. Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics. HORTICULTURE RESEARCH 2020; 7:117. [PMID: 32821400 PMCID: PMC7395147 DOI: 10.1038/s41438-020-0338-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/12/2020] [Accepted: 05/01/2020] [Indexed: 05/25/2023]
Abstract
Kiwifruit (Actinidia spp.) plants produce economically important fruits containing abundant, balanced phytonutrients with extraordinarily high vitamin C contents. Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species. To efficiently store, analyze, integrate, and disseminate these large-scale datasets to the research community, we constructed the Kiwifruit Genome Database (KGD; http://kiwifruitgenome.org/). The database currently contains all publicly available genome and gene sequences, gene annotations, biochemical pathways, transcriptome profiles derived from public RNA-Seq datasets, and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies. A set of user-friendly query interfaces, analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit, which include JBrowse, a popular genome browser, and the NCBI BLAST sequence search tool. Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology (GO) term and pathway enrichment analysis.
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Affiliation(s)
- Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
| | - Jiacheng Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Wei Tang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Ya Qing Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Xiaofeng Tang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
| | - Wei Li
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Lihuan Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Shengxiong Huang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
| | - Congbing Fang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064 China
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206 China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, 102206 China
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Vu DD, Shah SNM, Pham MP, Bui VT, Nguyen MT, Nguyen TPT. De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. BMC PLANT BIOLOGY 2020; 20:358. [PMID: 32727354 PMCID: PMC7391578 DOI: 10.1186/s12870-020-02571-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. RESULTS In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. CONCLUSION Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.
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Affiliation(s)
- Dinh Duy Vu
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University Dera Ismail Khan, Dera Ismail Khan, Pakistan
| | - Mai Phuong Pham
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Van Thang Bui
- College of Forestry Biotechnology, Vietnam National University of Forestry, Xuan Mai, Hanoi, Vietnam
| | - Minh Tam Nguyen
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Phuong Trang Nguyen
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, , Cau Giay, Hanoi, Vietnam.
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7
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He D, Zhang J, Zhang X, He S, Xie D, Liu Y, Li C, Wang Z, Liu Y. Development of SSR markers in Paeonia based on De Novo transcriptomic assemblies. PLoS One 2020; 15:e0227794. [PMID: 31999761 PMCID: PMC6991952 DOI: 10.1371/journal.pone.0227794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/30/2019] [Indexed: 12/31/2022] Open
Abstract
Peony is a famous ornamental and medicinal plant in China, and peony hybrid breeding is an important means of germplasm innovation. However, research on the genome of this species is limited, thereby hindering the genetic and breeding research on peony. In the present study, simple sequence repeat (SSR) locus analysis was performed on expressed sequence tags obtained by the transcriptome sequencing of Paeonia using Microsatellite software. Primers with polymorphism were obtained via polymerase chain reaction amplification and electrophoresis. As a result, a total of 86,195 unigenes were obtained by assembling the transcriptome data of Paeonia. Functional annotations were obtained in seven functional databases including 49,172 (Non-Redundant Protein Sequence Database: 57.05%), 38,352 (Nucleotide Sequence Database: 44.49%), 36,477 (Swiss Prot: 42.32%), 38,905 (Clusters of Orthologous Groups for Eukaryotic Complete Genomes: 45.14%), 37,993 (Kyoto Encyclopedia of Genes and Genomes: 44.08%), 26,832 (Gene Ontology: 31.13%) and 37,758 (Pfam: 43.81%) unigenes. Meanwhile, 21,998 SSR loci were distributed in 17,567 unigenes containing SSR sequences, and the SSR distribution frequency was 25.52%, with an average of one SSR sequence per 4.66 kb. Mononucleotide, dinucleotide, and trinucleotide were the main repeat types, accounting for 55.74%, 25.58%, and 13.21% of the total repeat times, respectively. Forty-five pairs of the 100 pairs of primers selected randomly could amplify clear polymorphic bands. The polymorphic primers of these 45 pairs were used to cluster and analyze 16 species of peony. The new SSR molecular markers can be useful for the study of genetic diversity and marker-assisted breeding of peony.
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Affiliation(s)
- Dan He
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Institute of Science and Technology, Postdoctor Research Base, Xinxiang, Henan, China
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiaorui Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuefeng Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Songlin He
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Institute of Science and Technology, Xinxiang, Henan, China
- * E-mail:
| | - Dongbo Xie
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yang Liu
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St Paul, Minnesota, United States of America
| | - Chaomei Li
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zheng Wang
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yiping Liu
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
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8
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Tang P, Shen R, He R, Yao X. The complete chloroplast genome sequence of Actinidia eriantha. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2114-2115. [PMID: 33365432 PMCID: PMC7687386 DOI: 10.1080/23802359.2019.1623111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The complete chloroplast (cp) genome sequence of Actinidia eriantha was sequenced and assembled using Illumina paired-end data. The cp genome from A. eriantha is 156,964 bp in length, composed of a pair of 23,892 bp inverted repeat regions (IR) separated by a large single copy region (LSC) of 88,639 bp and a small single copy region (SSC) of 20,541 bp. The cp genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four ribosomal RNA genes. The phylogenetic position of A. eriantha based the cp genome data was sister to the group A. rufa, A. deliciosa, and A. chinensis.
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Affiliation(s)
- Ping Tang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Hubei, China
| | - Ruinan Shen
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Hubei, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ruiwen He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Hubei, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Hubei, China
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9
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Tang W, Sun X, Yue J, Tang X, Jiao C, Yang Y, Niu X, Miao M, Zhang D, Huang S, Shi W, Li M, Fang C, Fei Z, Liu Y. Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. Gigascience 2019; 8:giz027. [PMID: 30942870 PMCID: PMC6446220 DOI: 10.1093/gigascience/giz027] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/12/2018] [Accepted: 03/01/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Kiwifruit (Actinidia spp.) is a dioecious plant with fruits containing abundant vitamin C and minerals. A handful of kiwifruit species have been domesticated, among which Actinidiaeriantha is increasingly favored in breeding owing to its superior commercial traits. Recently, elite cultivars from A. eriantha have been successfully selected and further studies on their biology and breeding potential require genomic information, which is currently unavailable. FINDINGS We assembled a chromosome-scale genome sequence of A. eriantha cultivar White using single-molecular sequencing and chromatin interaction map-based scaffolding. The assembly has a total size of 690.6 megabases and an N50 of 21.7 megabases. Approximately 99% of the assembly were in 29 pseudomolecules corresponding to the 29 kiwifruit chromosomes. Forty-three percent of the A. eriantha genome are repetitive sequences, and the non-repetitive part encodes 42,988 protein-coding genes, of which 39,075 have homologues from other plant species or protein domains. The divergence time between A. eriantha and its close relative Actinidia chinensis is estimated to be 3.3 million years, and after diversification, 1,727 and 1,506 gene families are expanded and contracted in A. eriantha, respectively. CONCLUSIONS We provide a high-quality reference genome for kiwifruit A. eriantha. This chromosome-scale genome assembly is substantially better than 2 published kiwifruit assemblies from A. chinensis in terms of genome contiguity and completeness. The availability of the A. eriantha genome provides a valuable resource for facilitating kiwifruit breeding and studies of kiwifruit biology.
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Affiliation(s)
- Wei Tang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, 29 Wang Jiang Lu, Sichuan University, Chengdu, Sichuan 610064, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Xuepeng Sun
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
| | - Junyang Yue
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Xiaofeng Tang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
| | - Xiangli Niu
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Min Miao
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Danfeng Zhang
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Shengxiong Huang
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Wei Shi
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Mingzhang Li
- Sichuan Academy of Natural Resource Sciences, 24 Yi Huan Lu Nan Er Duan, Chengdu, Sichuan 610015, China
| | - Congbing Fang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
- U.S. Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, 29 Wang Jiang Lu, Sichuan University, Chengdu, Sichuan 610064, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
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Wang X, Chen W, Luo J, Yao Z, Yu Q, Wang Y, Zhang S, Liu Z, Zhang M, Shen Y. Development of EST-SSR markers and their application in an analysis of the genetic diversity of the endangered species Magnolia sinostellata. Mol Genet Genomics 2018; 294:135-147. [PMID: 30255205 DOI: 10.1007/s00438-018-1493-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
Abstract
Magnolia sinostellata is an endemic species of Magnoliaceae that is narrowly distributed in the south of Zhejiang Province, China. To explore the genetic diversity and population structure of this endangered species, this study developed sequence tag-simple sequence repeat (EST-SSR) markers based on transcriptome data of M. sinostellata. In total, 25472 SSRs were identified among 110644 unique assembled sequences with a total of 90.83 Mb and an average frequency of 23.02%. The mononucleotide (33.53%) and dinucleotide (42.08%) motifs appeared to be the most abundant. In total, 150 potential loci were randomly selected to validate the quality of the developed SSR markers; an effective PCR rate of 32.00% and a polymorphism rate of 15.33% were obtained for these loci. After performing sequencing and cloning for validation, 23 pairs of SSR primers were retained and used to characterize the genetic diversity and population structure of M. sinostellata. Overall, 204 alleles were amplified. The results of Shannon's information index (I), heterozygosity (Ho), heterozygosity (He) and Nei's expected heterozygosity (H) indicated rich genetic diversity in M. sinostellata. However, the high inbreeding coefficient and differential coefficient suggest that serious genetic drift occurred within populations, and genetic differentiation is apparent among the populations. Consequently, although M. sinostellata has high genetic diversity among populations, it is still in a serious and dangerous condition. Habitat destruction caused by human activities is the main threat to this species, and enhancing the species abundance by adopting some conservation measures should be favourable for saving the species.
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Affiliation(s)
- Xingli Wang
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Wenchong Chen
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Jia Luo
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Zhangxiu Yao
- Shenzhen Fairy Lake Botanical Garden, 160# Xianhu Road, Shenzhen, 518004, Guangdong, China
| | - Qin Yu
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Yaling Wang
- Xi'an Botanical Garden of Shaanxi Academy of Science, 17# Cuihua South Road, Xi'an, 710061, Shaanxi, China
| | - Shouzhou Zhang
- Shenzhen Fairy Lake Botanical Garden, 160# Xianhu Road, Shenzhen, 518004, Guangdong, China
| | - Zhigao Liu
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Mingru Zhang
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China
| | - Yamei Shen
- School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin'an, 311300, Zhejiang, China.
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11
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Cheng J, Zhang N, Sha ZL. Isolation and characterization of microsatellite markers for exploring introgressive hybridization between the Oratosquilla oratoria complex. Mol Biol Rep 2018; 45:1499-1505. [PMID: 29948633 DOI: 10.1007/s11033-018-4208-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/05/2018] [Indexed: 12/11/2022]
Abstract
The Japanese mantis shrimp Oratosquilla oratoria is one of the most dominant stomatopod species found in coastal waters of the northwestern Pacific. We previously reported cryptic speciation and hybridization in this taxon by integrating mitochondrial and nuclear evidence. The present study aims at developing potential useful microsatellite markers for the O. oratoria complex through transcriptome sequencing, with a view to reveal the occurrence of hybridization. Of the 100 tested microsatellites, 55 were experimentally validated. 24 of these microsatellites were transferable across different species of the O. oratoria complex and showed polymorphic among individuals. The average number of alleles, observed and expected heterozygosity per locus was 6.125, 0.446 and 0.577 for the temperate species, and 6.083, 0.444 and 0.578 for the subtropical and tropical species. We also explore genetic differentiation and hybridization between O. oratoria cryptic species using these 24 microsatellite loci. The pairwise FST values and phylogenetic tree indicated a strong genetic differentiation between the two cryptic species. In addition, Bayesian analysis provided evidence for the presence of hybridization between the O. oratoria complex. These markers provide valuable genomic resources for exploring introgressive hybridization and expanding understanding of evolution in the O. oratoria complex.
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Affiliation(s)
- Jiao Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100039, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Nan Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhong-Li Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,University of Chinese Academy of Sciences, Beijing, 100039, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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