Transcriptome assembly of Richtersius coronifer with annotated BLAST result against Ramazzottius varieornatus.
datasetposted on 05.11.2019, 10:56 by Kazuharu Arakawa
For transcriptome sequencing and assembly, total RNA was extracted from a single specimen of tardigrade using Direct-zol RNA kit (Zymo Research) and was amplified using SMARTer Ultra Low Input RNA Kit for Sequencing v.3 (Clonetech). Illumina libraries were prepared using KAPA HyperPlus Kit (KAPA BIosystems), and the library was sequenced using a NextSeq 500 High Output Mode 75 cycles kit (Illumina) as single-end 75bp layout. Protocols are detailed in Arakawa et al. (2016)andYoshida et al. (2018). Sequences were filtered for adapters and demultiplexed using the bcl2fastq v.2 software (Illumina), and were assembled de novousing Bridger software with default parameters (Chang et al. 2015). Completeness of the assembly was assessed using BUSCO v.2/3 transcriptome mode with Eukaryote reference through gVolante server (Nishimura et al. 2017). Gene content was compared with Ramazzottius varieornatusand Hypsibius exemplaris genomes (Yoshida et al. 2017), as well as Drosophila melanogasterand Caenorhabditis elegansreference proteomes obtained from Flybase and Wormbase, respectively. Annotated BLAST result to R. varieornatus reference proteome with BLASTX (-e 1e-5) is also provided with the transcriptome assembly.