De novo assembly and characterization of the Hucho taimen transcriptome

Abstract

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 nonmodel 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 1,060 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 eight 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.

Transcriptome analysis provides insights into copper toxicology in piebald naked carp (Gymnocypris eckloni)

“…The number of transcripts obtained in this work is similar to many published transcriptome assemblies [ 13 , 17 – 21 ], including de novo transcriptome assemblies in several teleost species [ 13 , 20 , 21 ]. This indicates that our assembly quality is reliable to be used for subsequent transcriptome data analysis.…”

Evaluation of qPCR reference genes for taimen (Hucho taimen) under heat stress

“…Using the transcriptome published by Tong 8 , the transcript sequences of 10 genes, 28S rRNA , GAPDH , ARBPR , 18S rRNA , β - actin , RPS29 , RPL13 , RPL19 , Saha , and α-tubulin , were determined for qRT-PCR primer design. The primers were first designed using Primer3 https://primer3plus.com/ (Table 1 ) and then aligned to the taimen transcriptome using a BLAST search to confirm the specificity 32 .…”

“…Therefore, it is important to study the high-temperature tolerance mechanisms of taimen to optimize the production of this species, including breeding programs. Currently, many microsatellite 6 , 7 markers, transcriptomes obtained by mRNA sequencing 8 , high resolution linage maps 9 , and genome sequences of huchen, a closely related fish ( Hucho hucho , GCA_003317085.1 in GenBank) have been developed. These are useful tools to characterize candidate genes related to high-temperature tolerance.…”

Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey

“…To date, there is still no gold standard method for determining the quality of transcriptome assemblies for non-model organisms such as dinoflagellates. This study takes the approach suggested by Tong et al [ 27 ]. To evaluate the quality of the A. minutum unigenes, the raw reads were mapped back to the assembled unigenes using HISAT2, and the results showed that 80% of the total reads were mapped correctly.…”

“…This study used two methods to evaluate the quality of the A. minutum assembled unigenes: assessing the percentage of raw data mapping to the transcriptome assemblies and based on the conserved orthologue sequence content [ 27 ]. The HISAT2, a fast and sensitive alignment program for mapping sequence reads to transcriptome data sets, is used to evaluate the percentage of raw data re-mapping [ 28 ].…”