| De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn | |
| Tang, Hanqing; Saina, Josphat K.; Long, Zhi-Cheng; Chen, Jinming1; Dai, Can3 | |
| 2022 | |
| Source Publication | PEERJ
 |
| ISSN | 2167-8359 |
| Volume | 10Issue:xPages:- |
| Abstract | Background. Sagittaria trifolia Linn. is a widespread macrophyte in Asia and southeast Europe and cultivated in parts of Asia. Although a few genomic studies have been conducted for S. trifolia var. sinensis, a crop breed, there is limited genomic information on the wild species of S. trifolia. Effective microsatellite markers are also lacking. Objective. To assemble transcriptome sequence and develop effective EST-SSR markers for S. trifolia. Methods. Here we developed microsatellite markers based on tri-, tetra-, penta-, and hexa-nucleotide repeat sequences by comparatively screening multiple transcriptome sequences of eleven individuals from ten natural populations of S. trifolia. Results. A total of 107,022 unigenes were de novo assembled, with a mean length of 730 bp and an N50 length of 1,378 bp. The main repeat types were mononucleotide, trinucleotide, and dinucleotide, accounting for 55.83%, 23.51%, and 17.56% of the total repeats, respectively. A total of 86 microsatellite loci were identified with repeats of tri-, tetra-, penta-, and hexa-nucleotide. For SSR verification, 28 polymorphic loci from 41 randomly picked markers were found to produce stable and polymorphic bands, with the number of alleles per locus ranging from 2 to 11 and a mean of 5.2. The range of polymorphic information content (PIC) of each SSR locus varied from 0.25 to 0.80, with an average of 0.58. The expected heterozygosity ranged from 0.29 to 0.82, whereas the observed heterozygosity ranged from 0.25 to 0.90. Conclusion. The assembled transcriptome and annotated unigenes of S. trifolia provide a basis for future studies on gene functions, pathways, and molecular mechanisms associated with this species and other related. The newly developed EST-SSR markers could be effective in examining population genetic structure, differentiation, and parentage analyses in ecological and evolutionary studies of S. trifolia |
| Keyword | GENETIC-LINKAGE MAP ABSOLUTE STEREOSTRUCTURES ALISMATACEAE RESOURCE SUCCESS GROWTH PLANTS TUBER |
| Subject Area | Science & Technology - Other Topics |
| DOI | 10.7717/peerj.14268 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:000964827400005 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | https://ir.xtbg.ac.cn/handle/353005/13474 |
| Collection | 2012年后新成立研究组 |
| Affiliation | 1.Hubei Univ, Sch Resources & Environm Sci, Wuhan, Peoples R China 2.Chinese Acad Sci, Wuhan Bot Garden, Wuhan, Peoples R China 3.Hostgene Co Ltd, Wuhan, Peoples R China 4.Hubei Univ, Hubei Key Lab Reg Dev & Environm Response, Wuhan, Peoples R China 5.Saina, Josphat K.] Chinese Acad Sci, Ctr Integrat Conservat, Xishuangbanna Trop Bot Garden, Menglun, Peoples R China |
| Recommended Citation GB/T 7714 | Tang, Hanqing,Saina, Josphat K.,Long, Zhi-Cheng,et al. De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn[J]. PEERJ,2022,10(x):-. |
| APA | Tang, Hanqing,Saina, Josphat K.,Long, Zhi-Cheng,Chen, Jinming,&Dai, Can.(2022).De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn.PEERJ,10(x),-. |
| MLA | Tang, Hanqing,et al."De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn".PEERJ 10.x(2022):-. |
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| De novo transcriptom（8847KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Download | |
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