文献笔记二十八：猕猴桃（Kiwifruit）线粒体基因组

2019-05-11 本文已影响4人小明的数据分析笔记本

文章题目

Evolution and Diversification of Kiwifruit Mitogenomes through Extensive Whole-Genome Rearrangement and Mosaic Loss of Intergenic Sequences in a Highly Variable Region

发表时间、期刊及完成单位

GBE Genome Biology and Evolution
期刊简写：Genome Biol Evol
中科院2区 3.940
2019年3月18号 March 18, 2019
中科院华南植物园 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences.

当前阶段重点关注完整线粒体基因组的组装方法

植物材料 Plant Materials

Actinidia arguta
Actinidia chinensis
Actinidia eriantha

测序策略

Actinidia arguta ：分离线粒体提取线粒体DNA（Intact and pure mitochondria were isolated as previously reported. mtDNA was extract from purified mitochondria.）；both 250-bp paired-end library and 3-kb mate-pair library were prepared and sequenced on an illumina HiSeq 2500 platform.二代测序短片段库加长片段库。
Actinidia chinensis：分离线粒体提取线粒体DNA。三代测序（PacBio RS II long reads）
Actinidia eriantha：genomic DNA was extracted from fresh leaves.二代加三代。

数据存储

The raw data have been deposited at NCBI Sequence Read Archive under the accessions SRR7458400——SRR7458405

分析过程中用到的代码

All the source codes used for the analysis are provided at https://github.com/wangshuaibin1015/kiwifruit_mitogenomes

重复组装过程

下载原始测序数据（原始数据还没有公开）

CJ大神开发的工具Tbtools又开放了一个小工具：根据SRA number 获取原始数据的下载链接省事地获取已公开测序数据的下载链接（.sra|.fastq.gz），非常方便。之前自己需要下载时都是根据链接ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads，在找自己需要的数据。

组装策略

二代短片段加长片段文库 Actinidia arguta 使用SPAdes v3.10.1软件组装QUAST评估组装效果，最终选择k-mer127进行组装。结果：Finally, we identified only one candidate mitochondrial scaffold, which can be mapped as a circular molecule indicated by a pair of direct repeats at its both ends.