Complete mitochondrial genome of Siberian taimen, Hucho taimen not introgressed by the lenok subspecies, Brachymystax lenok and B. lenok tsinlingensis

De novo assembly and characterization of the Hucho taimen transcriptome

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.

Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information.

Complete mitochondrial genomes of the anadromous and resident forms of the lamprey Lethenteron camtschaticum

The complete mitochondrial genomes were sequenced in anadromous and resident forms of the lamprey Lethenteron camtschaticum. The sizes of the genomes in the two isolates are 16,245 and 16,295 bp. The gene arrangement, base composition, and size of the two sequenced genomes are similar to the lamprey genomes previously published. The total sequence divergence between the two genomes is very low (0.14%), supporting conspecificity of the anadromous and resident forms of L. camtschaticum. Comparison of the genomes sequenced in the present work with other genomes of lampreys available in GenBank, reveals two distinct evolutionary lineages with a genera level of divergence among the lampreys of eastern Eurasia.

Complete mitochondrial genome of Sakhalin taimen Parahucho perryi (Salmoniformes, Salmonidae) without two frame-disrupting indels in the ND4 gene

The complete mitochondrial genome was sequenced in two individuals of Sakhalin taimen Parahucho perryi. The genome sizes were 16,652 bp and 16,653 bp in the two isolates. Gene arrangement, base composition, and size of the two sequenced haplotypes are very similar to the P. perryi genome previously published (KC897653), but do not contain two frame-disrupting indels in the ND4 gene.