| Abstract Detail
Recent Topics Posters Jin, Jian-Jun [1], Yu, Wen-Bin [2], Yang, Jun-Bo [1], Song, Yu [3], Yi, Ting-Shuang [1], Li, De-Zhu [1]. GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data. Chloroplast genes and genomes are the most important genomic data for plant phylogeny and DNA barcoding. Since the rapid development of high throughput sequencing technologies, it is cheap to get the low coverage data of whole genome, which is enough to assemble a complete chloroplast genome. In this study, we reported a simple, fast and reliable procedure to assemble a circular chloroplast genome using GetOrganelle pipeline. The GetOrganelle pipeline consists of four steps: 1) recruiting plastid-like reads by extension; 2) de novo assembly using SPAdes; 3) filtering plastid-like contigs, and 4) visualizing and editing de novo assembly graph. Of them, the first three steps can be fulfilled automatically just using a combined command; and the fourth step is to visualize and evaluate the assemblies. Of 57 tested species with public datasets, we directly reassembled the circular chloroplast genome in 47 species. The nine non-circular species having breakpoints, which may be caused by mononucleotide or dinucleotide repeats, or small reads pool. Many published ones were misassembled at some sites, while our GetOrganelle results were generally more accurate. In addition, we successfully assembled the circular chloroplast genome for the other 903 species of angiosperms using this pipeline, representing 41 families and 358 genera. The GetOrganelle pipeline is an effective way for land plants to assemble the circular chloroplast genome, without needs for reference-guided scaffolding, gap filling nor start-end point closing. This pipeline can be also applied to assemble mitochondrial genomes and nuclear Ribosomal DNAs using the genome skimming data.
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Related Links:
https://www.biorxiv.org/content/early/2018/03/14/256479
BioRxiv preprint
1 - Kunming Institute of Botany, Chinese Academy of Sciences, Germplasm Bank of Wild Species, 132 Lanhei Road, Kunming, Yunnan, 650201, China
2 - Xishuangbanna Tropical Botanical Garden, Chinese Academy Of Sciences, Menglun, Mengla, Yunnan, 666303, China
3 - Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Center for Integrative Conservation, Menglun, Mengla, Yunnan, 666303, China
Keywords:
assembly
Bandage
Bowtie2
GetOrganelle
Organelle genome
plastome
SPAdes.
Presentation Type: Recent Topics Poster
Session: P, Recent Topics Posters
Location: Grand Ballroom - Exhibit Hall/Mayo Civic Center
Date: Monday, July 23rd, 2018
Time: 5:30 PM
Number: PRT009
Abstract ID:1288
Candidate for Awards:None |
