Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, ophiocordyceps sinensis
文献类型：期刊论文
| 作者 | Li, Yi1,2; Hsiang, Tom3; Yang, Rui-Heng1,4; Hu, Xiao-Di1,4; Wang, Ke1,4; Wang, Wen-Jing1; Wang, Xiao-Liang1; Jiao, Lei1; Yao, Yi-Jian1 |
| 刊名 | Journal of microbiological methods
 |
| 出版日期 | 2016-09-01 |
| 卷号 | 128页码:1-6 |
| 关键词 | Genome Sequencing Assembly Coverage Trimming Rna-seq |
| ISSN号 | 0167-7012 |
| DOI | 10.1016/j.mimet.2016.06.025 |
| 通讯作者 | Yao, yi-jian(yaoyj@im.ac.cn) |
| 英文摘要 | Ophiocordyceps sinensis is one of the most expensive medicinal fungi world-wide, and has been used as a traditional chinese medicine for centuries. in a recent report, the genome of this fungus was found to be expanded by extensive repetitive elements after assembly of roche 454 (223 mb) and illumina hiseq (10.6 gb) sequencing data, producing a genome of 87.7 mb with an n50 scaffold length of 12 kb and 6972 predicted genes. to test whether the assembly could be improved by deeper sequencing and to assess the amount of data needed for optimal assembly, genomic sequencing was run several times on genomic dna extractions of a single ascospore isolate (strain 1229) on an illumina hiseq platform (25 gb total data). assemblies were produced using different data types (raw vs. trimmed) and data amounts, and using three freely available assembly programs (abyss, soap and velvet). in nearly all cases, trimming the data for low quality base calls did not provide assemblies with higher n50 values compared to the non-trimmed data, and increasing the amount of input data (i.e. sequence reads) did not always lead to higher n50 values. depending on the assembly program and data type, the maximal n50 was reached with between 50% to 90% of the total read data, equivalent to 100 x to 200 x coverage. the draft genome assembly was improved over the previously published version resulting in a 114 mb assembly, scaffold n50 of 70 kb and 9610 predicted genes. among the predicted genes, 9213 were validated by rna-seq analysis in this study, of which 8896 were found to be singletons. evidence from genome and transcriptome analyses indicated that species assemblies could be improved with defined input material (e.g. haploid mono-ascospore isolate) without the requirement of multiple sequencing technologies, multiple library sizes or data trimming for low quality base calls, and with genome coverages between 100x and 200x. (c) 2016 elsevier b.v. all rights reserved. |
| WOS关键词 | RNA-SEQ ; OBLIGATE BIOTROPHY ; GENES |
| WOS研究方向 | Biochemistry & Molecular Biology ; Microbiology |
| WOS类目 | Biochemical Research Methods ; Microbiology |
| 语种 | 英语 |
| WOS记录号 | WOS:000382346300001 |
| 出版者 | ELSEVIER SCIENCE BV |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2375496 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Yao, Yi-Jian |
| 作者单位 | 1.Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, 1 Beichen West Rd, Beijing 100101, Peoples R China 2.Fujian Agr & Forestry Univ, Inst Plant Virol, Fujian Prov Key Lab Plant Virol, 15 Shangxiadian Rd, Fuzhou 350002, Peoples R China 3.Univ Guelph, Sch Environm Sci, 50 Stone Rd East, Guelph, ON N1G 2W1, Canada 4.Univ Chinese Acad Sci, 19 A Yuquan Rd, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Li, Yi,Hsiang, Tom,Yang, Rui-Heng,et al. Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, ophiocordyceps sinensis[J]. Journal of microbiological methods,2016,128:1-6. |
| APA | Li, Yi.,Hsiang, Tom.,Yang, Rui-Heng.,Hu, Xiao-Di.,Wang, Ke.,...&Yao, Yi-Jian.(2016).Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, ophiocordyceps sinensis.Journal of microbiological methods,128,1-6. |
| MLA | Li, Yi,et al."Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, ophiocordyceps sinensis".Journal of microbiological methods 128(2016):1-6. |
入库方式： iSwitch采集
来源：中国科学院大学
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。