ena-STUDY-European Bioinformatics Institute (EMBL-EBI) -18-08-2014-16:26:55:458-471
de novo Sequencing and annotation of the Culicoides sonorensis genome
The Culicoides biting midges include major vectors of livestock disease agents such as bluetongue virus (BTV), Schmallenberg virus and African horse sickness virus. These diseases are listed as notifiable by the World Organisation for Animal Health (OIE), a recognition of their potential for rapid spread via Culicoides dispersal and the clinical severity of the diseases they cause. Despite their relevance, Culicoides are a major family of biological vectors within the Diptera for which a genome sequence is not available. The closest phylogenetic species to the biting midges for which complete annotated genomes are available belong to the Culicidae, which have an estimated time of divergence of more than 200 million years. With the final aim of studying the genetic basis of vector competence in Culicoides species, we have generated the first de novo genome assembly of the KC cell line derived from the North American vector of bluetongue, Culicoides sonorensis. Two TrueSeq libraries with insert sizes of 180 and 600 bp, and two Nextera Mate Pair libraries with insert sizes of 3 and 8 kb, were sequenced on the Illumina HiSeq. Assembly and annotation of the genome was done using different software packages. The best results in terms of likelihood (ALE), fragment coverage distribution (REAPR) and feature response curves (FRCbam) were obtained using Velvet to assemble the contigs and SSPACE to build the scaffolds. The final assembly size of the genome is 209 Mb, distributed in 916 scaffolds with an N50 of 593 kbp. The predicted number of genes was 15512, similar number to that of A. gambiae and slightly smaller than the annotated genes in the D. melanogaster genome. We have identified 6198 orthologous groups between C. sonorensis KC cell line, D. melanogaster and A. gambiae, that included 10309 genes from the C. sonorensis cell line. This cell line genome will be validated sequencing the genomes of adult males and females of C. sonorensis.
The Culicoides biting midges include major vectors of livestock disease agents such as bluetongue virus (BTV), Schmallenberg virus and African horse sickness virus. These diseases are listed as notifiable by the World Organisation for Animal Health (OIE), a recognition of their potential for rapid spread via Culicoides dispersal and the clinical severity of the diseases they cause. Despite their relevance, Culicoides are a major family of biological vectors within the Diptera for which a genome sequence is not available. The closest phylogenetic species to the biting midges for which complete annotated genomes are available belong to the Culicidae, which have an estimated time of divergence of more than 200 million years. With the final aim of studying the genetic basis of vector competence in Culicoides species, we have generated the first de novo genome assembly of the KC cell line derived from the North American vector of bluetongue, Culicoides sonorensis. Two TrueSeq libraries with insert sizes of 180 and 600 bp, and two Nextera Mate Pair libraries with insert sizes of 3 and 8 kb, were sequenced on the Illumina HiSeq. Assembly and annotation of the genome was done using different software packages. The best results in terms of likelihood (ALE), fragment coverage distribution (REAPR) and feature response curves (FRCbam) were obtained using Velvet to assemble the contigs and SSPACE to build the scaffolds. The final assembly size of the genome is 209 Mb, distributed in 916 scaffolds with an N50 of 593 kbp. The predicted number of genes was 15512, similar number to that of A. gambiae and slightly smaller than the annotated genes in the D. melanogaster genome. We have identified 6198 orthologous groups between C. sonorensis KC cell line, D. melanogaster and A. gambiae, that included 10309 genes from the C. sonorensis cell line. This cell line genome will be validated sequencing the genomes of adult males and females of C. sonorensis.