Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species
文献类型：期刊论文
| 作者 | Xia, Yun3; Luo, Wei2,3; Yuan, Siqi1,3; Zheng, Yuchi3; Zeng, Xiaomao3 |
| 刊名 | BMC GENOMICS
 |
| 出版日期 | 2019-12-07 |
| 卷号 | 19期号:2018页码:886 |
| ISSN号 | 1471-2164 |
| 关键词 | Transcriptome Genome assembly MiSeq Amphibians Population genetics Next-generation sequencing |
| DOI | 10.1186/s12864-018-5329-y |
| 产权排序 | 1 |
| 文献子类 | Article |
| 英文摘要 | BackgroundEven though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a critical issue for ecological and evolutionary studies. However, the extent to which assembly strategy, read length, sequencing depth, and library layout produce a measurable effect on microsatellite marker development remains unclear. Here, we use six frog species for genome skimming and two frog species for transcriptome sequencing to develop microsatellite markers, and investigate the effect of different isolation strategies on the yield of microsatellites.ResultsThe results revealed that the number of isolated microsatellites increases with increased data quantity and read length. Assembly strategy could influence the yield and the polymorphism of microsatellite development. Larger k-mer sizes produced fewer total number of microsatellite loci, but these loci had a longer repeat length, suggesting greater polymorphism. However, the proportion of each type of nucleotide repeats was not affected; dinucleotide repeats were always the dominant type. Finally, the transcriptomic microsatellites displayed lower levels of polymorphisms and were less abundant than genomic microsatellites, but more likely to be functionally linked loci.ConclusionsThese observations provide deep insight into the evolution and distribution of microsatellites and how different isolation strategies affect microsatellite development using NGS. |
| URL标识 | 查看原文 |
| WOS关键词 | MUTATION-RATES ; ION TORRENT ; MARKERS ; GENERATION ; SIZE ; REPEATS ; SSRS ; VARIABILITY ; ECOLOGISTS ; SELECTION |
| WOS研究方向 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| 语种 | 英语 |
| 出版者 | BMC |
| WOS记录号 | WOS:000452734300006 |
| 源URL | [http://210.75.237.14/handle/351003/30082]  |
| 专题 | 食品安全与环境治理领域_中国科学院环境与应用微生物重点实验室 |
| 作者单位 | 1.Sichuan Univ Sci & Engn, Coll Bioengn, Zigong 643000, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China; 3.Chinese Acad Sci, Chengdu Inst Biol, Chengdu 610041, Sichuan, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Xia, Yun,Luo, Wei,Yuan, Siqi,et al. Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species[J]. BMC GENOMICS,2019,19(2018):886. |
| APA | Xia, Yun,Luo, Wei,Yuan, Siqi,Zheng, Yuchi,&Zeng, Xiaomao.(2019).Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species.BMC GENOMICS,19(2018),886. |
| MLA | Xia, Yun,et al."Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species".BMC GENOMICS 19.2018(2019):886. |
入库方式： OAI收割
来源：成都生物研究所
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