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Hajibarat Z, Saidi A, Zeinalabedini M, Mousapour Gorji A, Ghaffari MR, Shariati V, Ahmadvand R. Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars. PLoS One 2024; 19:e0303783. [PMID: 38787845 PMCID: PMC11125566 DOI: 10.1371/journal.pone.0303783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding.
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Affiliation(s)
- Zahra Hajibarat
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ahmad Mousapour Gorji
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Vahid Shariati
- National Institute of Genetic Engineering and Biotechnology, NIGEB Genome Center, Tehran, Iran
| | - Rahim Ahmadvand
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Yumoto K, Kanbe T, Saito Y, Kaneko S, Tsuda Y. Efficient PCR Amplification Protocol of Nuclear Microsatellites for Exuviae-Derived DNA of Cicada, Yezoterpnosia nigricosta. FRONTIERS IN INSECT SCIENCE 2021; 1:696886. [PMID: 38468883 PMCID: PMC10926516 DOI: 10.3389/finsc.2021.696886] [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: 04/18/2021] [Accepted: 06/04/2021] [Indexed: 03/13/2024]
Abstract
Although insect exuviae-based genetics is challenging, it can be a valuable method for obtaining reliable DNA resources by non-invasive sampling. This approach is especially effective when the target species is endangered/endemic or when sampling the adult is difficult. One example is cicadas, which during molt leave their exoskeletons on tree trunks, making them easily collectable. While cicada exuviae-derived DNA has previously been employed for mitochondrial DNA sequencing, this study aimed to develop a reliable method for the PCR amplification of nuclear microsatellite loci from cicada exuviae derived DNA for application in molecular ecology, conservation and population genetics. Five different PCR amplification protocols were performed, and the fragment patterns compared with those obtained using DNA extracted from adult individuals. Moreover, the relationship between the freshness of the exuviae and genotyping success was evaluated. TaKaRa LA Taq provided the best performance in the PCR amplification of DNA isolated from cicada exuviae and the electropherogram showed a clear fragment pattern that was equivalent to that obtained from the DNA extracted from the adult individual. This result suggests that cicada exuviae-derived DNA can be amplified by PCR and that multiple independent loci of nuclear DNA microsatellite markers can be easily genotyped. This study demonstrates that fresh cicada exuviae provide high quality DNA, which can be used for microsatellite genotyping. The methods developed in this study are applicable not only for cicada but other insect species for which exuviae are available. Thus, this study can make a significant contribution to insect sciences.
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Affiliation(s)
- Keisuke Yumoto
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Takashi Kanbe
- Systematic Entomology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoko Saito
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, Fukushima, Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
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Graham RE, Reyes-Betancort JA, Chapman MA, Carine MA. Inter-island differentiation and contrasting patterns of diversity in the iconic Canary Island sub-alpine endemic Echium wildpretii (Boraginaceae). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1877847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Rachael E. Graham
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - J. Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), C/Retama 2, Puerto de la Cruz, 38400, Tenerife, Spain
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Mark A. Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Manco R, Chiaiese P, Basile B, Corrado G. Comparative analysis of genomic- and EST-SSRs in European plum ( Prunus domestica L.): implications for the diversity analysis of polyploids. 3 Biotech 2020; 10:543. [PMID: 33235823 PMCID: PMC7679426 DOI: 10.1007/s13205-020-02513-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/27/2020] [Indexed: 11/23/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.
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Wong GKS, Soltis DE, Leebens-Mack J, Wickett NJ, Barker MS, Van de Peer Y, Graham SW, Melkonian M. Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:741-765. [PMID: 31851546 DOI: 10.1146/annurev-arplant-042916-041040] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case theViridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C4 photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.
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Affiliation(s)
- Gane Ka-Shu Wong
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada;
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Douglas E Soltis
- Florida Museum of Natural History, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, Illinois 60022, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Michael Melkonian
- Faculty of Biology, University of Duisburg-Essen, D-45141 Essen, Germany
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Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach. Genomics 2019; 112:2041-2051. [PMID: 31770586 DOI: 10.1016/j.ygeno.2019.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/29/2019] [Accepted: 11/22/2019] [Indexed: 11/21/2022]
Abstract
Small cardamom (Elettaria cardamomum), grown in limited coastal tropical countries is one of the costliest and widely exported agri-produce having global turnover of >10 billion USD. Mosaic/marble disease is one of the major impediments that requires understanding of disease at molecular level. Neither whole genome sequence nor any genomic resources are available, thus RNA seq approach can be a rapid and economical alternative. De novo transcriptome assembly was done with Illumina Hiseq data. A total of 5317 DEGs, 2267 TFs, 114 pathways and 175,952 genic region putative markers were obtained. Gene regulatory network analysis deciphered molecular events involved in marble disease. This is the first transcriptomic report revealing disease mechanism mediated by perturbation in auxin homeostasis and ethylene signalling leading to senescence. The web-genomic resource (SCMVTDb) catalogues putative molecular markers, candidate genes and transcript information. SCMVTDb can be used in germplasm improvement against mosaic disease in endeavour of small cardamom productivity. Availability of genomic resource, SCMVTDb: http://webtom.cabgrid.res.in/scmvtdb/.
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Chapman MA. Optimizing depth and type of high-throughput sequencing data for microsatellite discovery. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11298. [PMID: 31832281 PMCID: PMC6858294 DOI: 10.1002/aps3.11298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Simple sequence repeat (SSR) markers (microsatellites) are a mainstay of many labs, especially when working on a limited budget, carrying out preliminary analyses, and in teaching. Whether SSRs mined from plant genomes or transcriptomes are preferred for certain applications, and the depth of sequencing needed to allow efficient SSR discovery, has not been tested. METHODS I used genome and transcriptome high-throughput sequencing data at a range of sequencing depths to compare efficacy of SSR identification. I then tested primers from tomato for amplification, polymorphism, and transferability to related species. RESULTS Small assemblies (two million read pairs) identified ca. 200-2000 potential markers from the genome assemblies and ca. 600-3650 from the transcriptome assemblies. Genome-derived contigs were often short, potentially precluding primer design. Genomic SSR primers were less transferable across species but exhibited greater variation (partially explained by being composed of more repeat units) than transcriptome-derived primers. DISCUSSION Small high-throughput sequencing resources may be sufficient for identification of hundreds of SSRs. Genomic data may be preferable in species with low polymorphism, but transcriptome data may result in longer loci (more amenable to primer design) and primers may be more transferable to related species.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUnited Kingdom
- Centre for Underutilised CropsUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUnited Kingdom
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An RNA Sequencing Transcriptome Analysis and Development of EST-SSR Markers in Chinese Hawthorn through Illumina Sequencing. FORESTS 2019. [DOI: 10.3390/f10020082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chinese hawthorn (Crataegus pinnatifida) is an important ornamental and economic horticultural plant. However, the lack of molecular markers has limited the development and utilization of hawthorn germplasm resources. Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) allow precise and effective cultivar characterization and are routinely used for genetic diversity analysis. Thus, we first reported the development of polymorphic EST-SSR markers in C. pinnatifida with perfect repeats using Illumina RNA-Seq technique. In total, we investigated 14,364 unigenes, from which 5091 EST-SSR loci were mined. Di-nucleotides (2012, 39.52%) were the most abundant SSRs, followed by mono- (1989, 39.07%), and tri-nucleotides (1024, 20.11%). On the basis of these EST-SSRs, a total of 300 primer pairs were designed and used for polymorphism analysis in 70 accessions collected from different geographical regions of China. Of 239 (79.67%) pairs of primer-generated amplification products, 163 (54.33%) pairs of primers showed polymorphism. Finally, 33 primers with high polymorphism were selected for genetic diversity analysis and tested on 70 individuals with low-cost fluorescence-labeled M13 primers using capillary electrophoresis genotyping platform. A total of 108 alleles were amplified by 33 SSR markers, with the number of alleles (Na) ranging from 2 to 14 per locus (mean: 4.939), and the effective number of alleles (Ne) ranging from 1.258 to 3.214 (mean: 2.221). The mean values of gene diversity (He), observed heterozygosity (Ho), and polymorphism information content (PIC) were 0.524 (range 0.205–0.689), 0.709 (range 0.132–1.000), and 0.450 (range 0.184–0.642), respectively. Furthermore, the dendrogram constructed based on the EST-SSR separated the cultivars into two main clusters. In sum, our study was the first comprehensive study on the development and analysis of a large set of SSR markers in hawthorn. The results suggested that the use of NGS techniques for SSR development represented a powerful tool for genetic studies. Additionally, fluorescence-labeled M13 markers proved to be a valuable method for genotyping. All of these EST-SSR markers have agronomic potential and constitute a scientific basis for future studies on the identification, classification, and innovation of hawthorn germplasms.
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Park S, Son S, Shin M, Fujii N, Hoshino T, Park S. Transcriptome-wide mining, characterization, and development of microsatellite markers in Lychnis kiusiana (Caryophyllaceae). BMC PLANT BIOLOGY 2019; 19:14. [PMID: 30621589 PMCID: PMC6325733 DOI: 10.1186/s12870-018-1621-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 12/27/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Lychnis kiusiana Makino is an endangered perennial herb native to wetland areas in Korea and Japan. Despite its conservational and evolutionary significance, population genetic resources are lacking for this species. Next-generation sequencing has been accepted as a rapid and cost-effective solution for the identification of microsatellite markers in nonmodel plants. RESULTS Using Illumina HiSeq 2000 sequencing technology, we assembled 67,498,600 reads into 91,900 contigs and identified 11,403 microsatellite repeat motifs in 9563 contigs. A total of 4510 microsatellite-containing transcripts had Gene Ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 124 pathways with significant scores. Many microsatellites in the L. kiusiana leaf transcriptome were linked to genes involved in the plant response to light intensity, salt stress, temperature stimulus, and nutrient and water deprivation. A total of 12,486 single-nucleotide polymorphisms (SNPs) were identified on transcripts harboring microsatellites. The analysis of nucleotide substitution rates for 2389 unigenes indicated that 39 genes were under strong positive selection. The primers of 6911 microsatellites were designed, and 40 of 50 selected primer pairs were consistently and successfully amplified from 51 individuals. Twenty-five of these were polymorphic, and the average number of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to 0.827, respectively, and locus-specific FIS estimates ranged from - 0.116 to 0.290. Eleven of the 25 primer pairs were successfully amplified in three additional species of Lychnis: 56% in L. wilfordii, 64% in L. cognata and 80% in L. fulgens. CONCLUSIONS The transcriptomic SSR markers of Lychnis kiusiana provide a valuable resource for understanding the population genetics, evolutionary history, and effective conservation management of this species. Furthermore, the identified microsatellite loci linked to the annotated genes should be useful for developing functional markers of L. kiusiana. The developed markers represent a potentially valuable source of transcriptomic SSR markers for population genetic analyses with moderate levels of cross-taxon portability.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk 38541 South Korea
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541 South Korea
| | - Sungwon Son
- Plant Conservation Division, Korea National Arboretum, Pocheon, Gyeonggi 11186 South Korea
| | - Myungju Shin
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541 South Korea
| | - Noriyuki Fujii
- Department of Biological Science, Graduate School of Science and Technology, Kumamoto University, Chuo-ku, Kumamoto, 860-8555 Japan
| | - Takuji Hoshino
- Faculty of Biosphere-Geosphere Science, Okayama University of Science, Kita-ku, Okayama, 700-0005 Japan
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541 South Korea
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Li J, Guo H, Wang Y, Zong J, Chen J, Li D, Li L, Wang J, Liu J. High-throughput SSR marker development and its application in a centipedegrass (Eremochloa ophiuroides (Munro) Hack.) genetic diversity analysis. PLoS One 2018; 13:e0202605. [PMID: 30133524 PMCID: PMC6105027 DOI: 10.1371/journal.pone.0202605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/05/2018] [Indexed: 11/18/2022] Open
Abstract
Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is a perennial, warm-season C4 grass species that shows great potential for use as a low-maintenance turfgrass species in tropical and subtropical regions. However, limited genetic and genomic information is available for this species, which has impeded systematic studies on the enhancement of its turf quality and resistance against biotic and abiotic stress. In this study, Illumina HiSeq high-throughput sequencing technology was performed to generate centipedegrass transcriptome sequences. A total of 352,513 assembled sequences were used to search for simple sequence repeat (SSR) loci, and 64,470 SSR loci were detected in 47,638 SSR containing sequences. The tri-nucleotides were the most frequent repeat motif, followed by di-nucleotides, tetra-nucleotides hexnucleotides, and pentanucleotides. A total of 48,061 primer pairs were successfully designed in the flanking sequences of the SSRs, and 100 sets of primers were randomly selected for the initial validation in four centipedegrass accessions. In total, 56 (56.0%) of the 100 primer pairs tested successfully amplified alleles from all four centipedegrass accessions, while 50 were identified as polymorphic markers and were then used to assess the level of genetic diversity among 43 centipedegrass core collections. The genetic diversity analysis exhibited that the number of alleles (Na) per locus ranged from 3 to 13, and the observed heterozygosity (Ho) ranged from 0.17 to 0.83. The polymorphism information content (PIC) value of the markers ranged from 0.15 to 0.78, and the genetic distances (coefficient Nei72) between the accessions varied from 0.07 to 0.48. The UPGMA-based dendrogram clustered all 43 core collections into two main groups and six subgroups, which further validated the effectiveness of these newly developed SSR markers. Hence, these newly developed SSR markers will be valuable and potentially useful for future genetic and genomic studies of E. ophiuroides.
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Affiliation(s)
- Jianjian Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Yi Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Dandan Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Ling Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingjing Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
- * E-mail:
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Liu L, Wang Y, He P, Li P, Lee J, Soltis DE, Fu C. Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data. BMC Genomics 2018; 19:235. [PMID: 29618324 PMCID: PMC5885378 DOI: 10.1186/s12864-018-4633-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. Results The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. Conclusions In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4633-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Yuewen Wang
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Peizi He
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, 34134, South Korea
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering. Sci Rep 2017; 7:17598. [PMID: 29242627 PMCID: PMC5730610 DOI: 10.1038/s41598-017-16810-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/15/2017] [Indexed: 12/17/2022] Open
Abstract
The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves (Rhizophora mangle) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences. For all datasets, we calculated population genetic statistics and evaluated population structure, and for RAD-Seq datasets, we additionally examined population structure using coalescence. We found higher FST using microsatellites, but that RAD-Seq-based estimates approached those based on microsatellites as more loci with more missing data were included. Analyses of RAD-Seq datasets resolved the classic Gulf-Atlantic coastal phylogeographic break, which was not significant in the microsatellite analyses. Applying multiple levels of filtering to RAD-Seq datasets can provide a more complete picture of potential biases in the data and elucidate subtle phylogeographic patterns.
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Hou S, Sun Z, Li Y, Wang Y, Ling H, Xing G, Han Y, Li H. Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet ( Panicum miliaceum; Poaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600137. [PMID: 28791202 PMCID: PMC5546162 DOI: 10.3732/apps.1600137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 05/02/2017] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Proso millet (Panicum miliaceum; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers. METHODS Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple sequence repeat (SSR) markers were identified and used to detect polymorphism among 56 accessions. Population structure and genetic similarity coefficient were estimated. RESULTS In total, 25,341 unique gene sequences and 4724 SSR loci were obtained from the transcriptome, of which 229 pairs of SSR primers were validated, which resulted in 14 polymorphic genic SSR primers exhibiting 43 total alleles. According to the ratio of polymorphic markers (6.1%, 14/229), there are potentially 288 polymorphic genic SSR markers available for genetic assay development in the future. Bayesian population analyses showed that the 56 accessions comprised two distinct groups. DISCUSSION A genetic structure and cluster assay indicated that the accessions from the Loess Plateau of China shared a high genetic similarity coefficient with those from other regions and that there was no correlation between genetic diversity and geographic origin. The transcriptome sequencing data and millet-specific SSR markers developed in this study establish an excellent resource for gene discovery and may improve the development of breeding programs in proso millet in the future.
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Affiliation(s)
- Siyu Hou
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taigu, Shanxi 030801, People’s Republic of China
| | - Zhaoxia Sun
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Yaoshen Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Yijie Wang
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Hubin Ling
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
| | - Guofang Xing
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taigu, Shanxi 030801, People’s Republic of China
| | - Yuanhuai Han
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on the Loess Plateau, Ministry of Agriculture, Institute of Crop Genetic Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi 030031, People’s Republic of China
| | - Hongying Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi 030801, People’s Republic of China
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Ren J, Su ZZ, Dang ZH, Ding Y, Wang PX, Niu JM. Development and characterization of EST-SSR markers in Stipa breviflora (Poaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600157. [PMID: 28439477 PMCID: PMC5400433 DOI: 10.3732/apps.1600157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/08/2017] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Stipa breviflora (Poaceae) is one of the dominant species of the desert steppe in the eastern Eurasian grasslands. Simple sequence repeat (SSR) markers were developed for use in genetic diversity studies of this species. METHODS AND RESULTS A total of 1954 potentially polymorphic loci were obtained by comparing transcriptome data of eight different S. breviflora individuals. We selected 81 loci to verify polymorphism and 63 loci amplified, of which 21 loci exhibited polymorphism. The number of alleles per locus varied from two to 24, the observed heterozygosity ranged from 0.083 to 0.958, and the expected heterozygosity ranged from 0.396 to 0.738. CONCLUSIONS These newly identified SSR loci can be used for population genetic and landscape genetic studies of S. breviflora. In addition, 14 loci also amplified in six related Stipa species (S. grandis, S. krylovii, S. bungeana, S. aliena, S. gobica, and S. purpurea).
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Affiliation(s)
- Jing Ren
- School of Ecology and Environmental Sciences, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Zhi-Zhen Su
- School of Ecology and Environmental Sciences, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Zhen-Hua Dang
- School of Ecology and Environmental Sciences, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Yu Ding
- School of Ecology and Environmental Sciences, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Pei-Xuan Wang
- School of Ecology and Environmental Sciences, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Jian-Ming Niu
- School of Ecology and Environmental Sciences, Inner Mongolia University, Hohhot, People’s Republic of China
- Sino-US Center for Conservation, Energy, and Sustainability Science, Inner Mongolia University, Hohhot, People’s Republic of China
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Mayland-Quellhorst E, Meudt HM, Albach DC. Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600091. [PMID: 27785388 PMCID: PMC5077287 DOI: 10.3732/apps.1600091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/02/2016] [Indexed: 05/24/2023]
Abstract
PREMISE OF THE STUDY Polyploidy may generate novel variation, leading to adaptation and species diversification. An excellent natural system to study polyploid evolution in a comparative framework is Veronica (Plantaginaceae), which comprises several parallel, recently evolved polyploid series. METHODS Over 105 million Illumina paired-end sequence reads were generated from cDNA libraries of leaf tissue from eight individuals representing three European and four New Zealand species. Forty-eight simple sequence repeat (SSR) and 48 low-copy nuclear (LCN) markers were developed and validated with Fluidigm microfluidic PCR and Illumina MiSeq amplicon sequencing on 48 different individuals each. RESULTS Individual Trinity assemblies were similar regarding annotated transcripts (13,009-14,271), mean contig length (635-742 bp), N50 value (916-1133 bp), E90N50 value (1099-1308 bp), contigs with positive BLAST hits (42-63%), and gene ontology terms. Analyses of 29,738 single-nucleotide polymorphisms (8746 phylogenetically informative) mined from these transcriptomes plus two outgroups (Picrorhiza kurrooa and Plantago ovata) showed moderate to high bootstrap support for all branches and reticulation among sampled European Veronica. DISCUSSION The transcriptome sequences themselves, as well as the validated SSR (40/48) and LCN (11/48) markers derived from them, show inter- and intraspecific genetic variation. These resources will be invaluable for future population genetic, phylogenetic, and functional genetic investigations in polyploid Veronica.
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Affiliation(s)
- Eike Mayland-Quellhorst
- Carl-von-Ossietzky Universität Oldenburg, Carl-von-Ossietzky Straße 9–11, Oldenburg 26111, Germany
| | - Heidi M. Meudt
- Carl-von-Ossietzky Universität Oldenburg, Carl-von-Ossietzky Straße 9–11, Oldenburg 26111, Germany
- Museum of New Zealand Te Papa Tongarewa, Cable Street, P.O. Box 467, Wellington 6140, New Zealand
| | - Dirk C. Albach
- Carl-von-Ossietzky Universität Oldenburg, Carl-von-Ossietzky Straße 9–11, Oldenburg 26111, Germany
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Hodel RGJ, Segovia-Salcedo MC, Landis JB, Crowl AA, Sun M, Liu X, Gitzendanner MA, Douglas NA, Germain-Aubrey CC, Chen S, Soltis DE, Soltis PS. The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600025. [PMID: 27347456 PMCID: PMC4915923 DOI: 10.3732/apps.1600025] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.
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Affiliation(s)
- Richard G. J. Hodel
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- Author for correspondence:
| | | | - Jacob B. Landis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Andrew A. Crowl
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Xiaoxian Liu
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | | | - Norman A. Douglas
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | | | - Shichao Chen
- College of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
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