DOI: 10.5061/dryad.9gd3n
title: Data from: De novo assembly and characterization of the Hucho taimen transcriptome

description: Taimen (Hucho taimen) is an important ecological and economic species that
 is classified as vulnerable by the IUCN Red List of Threatened Species;
 however, limited genomic information is available on this species. RNA-Seq
 is a useful tool for obtaining genetic information and developing genetic
 markers for non-model species in addition to its application in gene
 expression profiling. In this study, we performed a comprehensive RNA-Seq
 analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them
 to de novo assemble a high-quality transcriptome with a N50 size of 1060
 bp. In the assembly, 82% of the transcripts were annotated using several
 databases, and 14,666 of the transcripts contained a full open reading
 frame. The assembly covered 75% of the transcripts of Atlantic salmon and
 57.3% of the protein-coding genes of rainbow trout. To learn about the
 genome evolution, we performed a systematic comparative analysis across 11
 teleosts including 8 salmonids, and found 313 unique gene families in
 taimen. Using Atlantic salmon and rainbow trout transcriptomes as the
 background, we identified 250 positive selection transcripts. The pathway
 enrichment analysis revealed a unique characteristic of taimen: it
 possesses more immune-related genes than Atlantic salmon and rainbow
 trout; moreover, some genes have undergone strong positive selection. We
 also developed a pipeline for identifying microsatellite marker genotypes
 in samples, and successfully identified 24 polymorphic microsatellite
 markers for taimen. These data and tools are useful for studying
 conservation genetics, phylogenetics, evolution among salmonids and
 selective breeding for threatened taimen.
description: Trinotate
 annotationThe taimen transcirptome
 was annotated using Trinotate(https://trinotate.github.io/) according to
 the guidance. NR, Uniprot-Sprot and Pfam databases were
 used.Trinotate.tsv.zipInterproscan annotationInterproscan annotation for taimen transcriptome. 79,800 transcripts were annotated using Interproscan.Interproscan.tsv.zipGene Ontology annotationThe sequences with significant hits in the Uniprot database or Pfam database were assigned GO terms using the Trinotate package, and the GO terms were assigned using Interproscan.72,728 transcripts were assigned to 15,107 GO terms, including 10,185 biological process terms, 1,429 cellular component terms and 3,493 molecular function terms.GO.txt.zipKEGG annotationA KEGG pathway analysis was performed using GhostKOALA . A total of 51,698 transcripts were assigned to 8,052 KEGG ortholog groupsKEGG.txt.zipeggNOG annotationThe COG functional category annotation using eggNOG-mapper (Huerta-Cepas et al., 2017), 72,605 putative proteins were annotated.eggNOG-mapper.tsv.zipAssembly transcriptomeThe transcriptome sequences were assembled using the Trinity package. Before assembly, low-quality reads were filtered from the raw reads using Trimmomatic with the parameters LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50. The clean reads from the two pooled libraries were merged and in silico normalized using the Trinity package with default parameters to reduce the running time and memory consumption. A parameter kmer size of 25 and a depth of at least two kmer were used for assembly with the Trinity package. The contigs resulting from Trinity were further fed to the TGI clustering Tool (version 2.1) to process alternative splicing and redundant sequences.The raw RNA-Seq reads and assembled transcripts were deposited in the European Nucleotide Archive under the project ID PRJEB19675 and accession numbers HAGJ01000001 to HAGJ01190473 for the assembled transcripts.transcriptome.embl.dat.zipSNP.vcfClean reads were firstly mapped to transcripts using Bowtie2, then SNPs were called SNPs using SAMtools. Raw SNPs with a minimum depth of 4 and minimum quality of 20 were filtered out using Vcftools (Danecek et al., 2011), and SNPs clustered within 50 bp were also filtered out. SNPs were annotated using snpEFF(http://snpeff.sourceforge.net/)ORF predictionTransDecoder (https://transdecoder.github.io/) was used to predict the open reading frames (ORFs) and translate proteins, and homology searches against pFam and Uniprot databases were performed as supporting evidence for the ORFs. The ORFs with fewer than 30 amino acids were discarded.TransDecoder.zipMicrosatellite PrimersSputnik software was used to search di-, tri-, tetra-, pena- and hex-nucleotide motif SSRs. Primers were designed using the Primer3 package.After aligning the amplicon sequences to the Atlantic salmon genome with BLAT, primers were chose because their amplicons were located in the genome of Atlantic salmon with identities &gt;70% and spanned distances close to the length of the amplicons.SSR.primers.txt.zipSequences of index and primersThis pack contains 4 files, "forward_index.txt" and "reverse_index" are index sequences for demultiplexing reads to samples, and "primers.txt" was primer sequences for classifying reads to loci, and "sample_config.txt" is index config for samples. These files were used to genotype 32 taimen samples which collected from the Hutou section of the Wusuli River (E133˚40´17″, N45˚58´50˝) . The raw reads sequenced with Illumina HiSeq2500 platform in 250 Pair-End mode were deposited to in the European Nucleotide Archive under the project ID PRJEB19675 with accession number ERR2029723.Index_and_primers_for_genotype.zipPipeline for characterizing polymorphism and defining genotype of microsatellite markersThis pack contains DeMultiIndex binary files, SSRGeno binary files(Linux 64 bit and MacOS 64bit system), an R script for drawing allele depth barplot and a manual document.microsatellite_pipeline.zip