Whole Genome Assembly and Annotation of the Giant Grouper, Epinephelus lanceolatus in Next Generation Sequencing
Date Issued
2014
Date
2014
Author(s)
Chen, Kuan-Ying
Abstract
Giant grouper (Epinephelus lanceolatus) is one of the most economically valuable aquaculture species in Taiwan. Its genome is estimated in 1.1G and has not been fully sequenced. In this study, we apply next-generation sequencing (NGS) technology to obtain whole genome shotgun sequences, then to do de novo assembly for recover the genome of E. lanceolatus from short reads. Then we annotate the genome of E. lanceolatus. Four different assembly strategies are evaluated for the best one to conclude genome scaffold. We chose ALLPATHS-LG as the assembler and used GapCloser to further fill the intra-scaffold gaps. Total 13,897 scaffolds, in total length sum of 1.09 G bp, were derived, from which 42,433 putative protein coding genes were predicted by AUGUSTUS using gene model of sea lamprey (Petromyzon marinus). Overall 92.6% of the protein products were annotated by nr (blastp, E-value: 1E-5). Among these best matched nr sequences, more than two-thirds protein coding sequences are from Phylum Actinopterygii, and the other one-third match to bacterial proteins. It indicate a possible source of sample contamination. We further remove scaffolds of bacterial origin and the final set is 9,473 scaffolds, sum up to 1.06 G bp; 29,184 protein sequences were derived and 89.3% of the best matched sequences were from Phylum Actinopterygii. There are 26,328 protein sequences mapped on KEGG database. We further annotated these protein sequences using Pfam, SignalP and tmHMM to reveal protein structure information. We use the whole set of protein coding genes derived from E. lanceolatus, Fugu rubripes, Danio rerio and Oreochromis niloticus and find the best hits for each proteins mutually by blast. About 80% of the protein sequences can find match between any two species.
Finally, we integrated the protein coding sequences with their annotations into a web database. This database will be open and become a helpful grouper genome resource for research community. It will benefit the grouper researchers for studying physiology and pathology, as well as for defining genetic traits such as fast growing rate and disease resistance for breeding.
Subjects
龍膽石斑
次世代定序
基因體定序
組裝
註解
Type
thesis
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