ena-STUDY-INSTITUTE OF INFORMATION SCIENCE, Academia Sinica-23-03-2018-16:31:55:249-2458
We have assembled the first version of Japanese eel genome as 1.06 Gb with 10,158 scaffolds, N50 over 1.4 Mb and coverage up to 122x from the blood of female yellow eel. By taking 1,211 scaffolds in length larger than 100Kb, these scaffolds can composite 92% of Japanese eel genome.
Common eel (or Japanese eel, Anguilla japonica) is an important aquaculture species with high economic value. It is a typical catadromous fish, spend most of the growth phase in fresh water and spawns in the ocean. It is a dramatic switch in habitats during the life cycle of A. japonica, coupled with the sex maturation and spawning migration. To know more about the mystery of their life cycle related with behavior, sex determination, reproduction and osmo-regulation on molecular level, there is a need to construct a completed genome as basis at first for omics studies. Then we can estimate the expression profiling under different spatiotemporal scenarios during their life cycle to realize the groups of genes which may regulate physiological phenomena. In past years, our team had built a transcriptome draft using RNA-seq from a sample pool of fertilized eggs, preleptocephalus, leptocephalus and glass eel stages with 300M Pair reads, 58 billion bases. The transcriptome information was implemented into a web database (http://molas.iis.sinica.edu.tw/jpeel, PLoS ONE, 2015) with rich annotations and a user-friendly interface.    Meanwhile, we have assembled the first version of Japanese eel genome as 1.06 Gb with 10,158 scaffolds, N50 over 1.4 Mb and coverage up to 122x from the blood of female yellow eel. By taking 1,211 scaffolds in length larger than 100Kb, these scaffolds can composite 92% of Japanese eel genome.   For accelerating assembly process and elevating the quality of genome, we also developed a new algorithm named as QReadSelector to extract the raw reads with less errors and shorten the time for assembling (https://github.com/moneycat/QReadSelector, BMC Genomic, 2015). According to transcriptome we assembled previously and those proteins of bony fishes from Uniprot, we construct the 27,350 gene models for Japanese Eel genome. After performing the similarity search with non-Redundancy database, eighty-two percent of best hits can be found in Actinopterii. And the top3 species are Asian Arowana (Scleropages formosus, 15%), Spotted gar (Lepisosteus oculatus, 13%), and Atlantic Salmon (Salmo salar,10%). Currently we have completed the web database for this first draft of Japanese eel genome with transcriptome (http://molas.iis.sinica.edu.tw/jpeel2016).
Common eel (or Japanese eel, Anguilla japonica) is an important aquaculture species with high economic value. It is a typical catadromous fish, spend most of the growth phase in fresh water and spawns in the ocean. It is a dramatic switch in habitats during the life cycle of A. japonica, coupled with the sex maturation and spawning migration. To know more about the mystery of their life cycle related with behavior, sex determination, reproduction and osmo-regulation on molecular level, there is a need to construct a completed genome as basis at first for omics studies. Then we can estimate the expression profiling under different spatiotemporal scenarios during their life cycle to realize the groups of genes which may regulate physiological phenomena. In past years, our team had built a transcriptome draft using RNA-seq from a sample pool of fertilized eggs, preleptocephalus, leptocephalus and glass eel stages with 300M Pair reads, 58 billion bases. The transcriptome information was implemented into a web database (http://molas.iis.sinica.edu.tw/jpeel, PLoS ONE, 2015) with rich annotations and a user-friendly interface.    Meanwhile, we have assembled the first version of Japanese eel genome as 1.06 Gb with 10,158 scaffolds, N50 over 1.4 Mb and coverage up to 122x from the blood of female yellow eel. By taking 1,211 scaffolds in length larger than 100Kb, these scaffolds can composite 92% of Japanese eel genome.   For accelerating assembly process and elevating the quality of genome, we also developed a new algorithm named as QReadSelector to extract the raw reads with less errors and shorten the time for assembling (https://github.com/moneycat/QReadSelector, BMC Genomic, 2015). According to transcriptome we assembled previously and those proteins of bony fishes from Uniprot, we construct the 27,350 gene models for Japanese Eel genome. After performing the similarity search with non-Redundancy database, eighty-two percent of best hits can be found in Actinopterii. And the top3 species are Asian Arowana (Scleropages formosus, 15%), Spotted gar (Lepisosteus oculatus, 13%), and Atlantic Salmon (Salmo salar,10%). Currently we have completed the web database for this first draft of Japanese eel genome with transcriptome (http://molas.iis.sinica.edu.tw/jpeel2016).