EST dataset of pituitary and identification of somatolactin and novel genes in Chinese sturgeon, Acipenser sinensis

Abstract

Chinese sturgeon (Acipenser sinensis) is a rare and endangered species and also an important resource for the sturgeon aquaculture industry, however, a few genes have been identified in this species. We report here construction of a pituitary cDNA library from a 24 years old female Chinese sturgeon just after its spawning, and obtained 2,025 ESTs from the library. 885 unique sequences were identified, which were categorized into 12 functional groups. More than half of the unique sequences (57%) do not match with annotated sequences in the public databases. Three of these novel genes were further identified. Notably, a full-length of cDNA (1,143 bp) encoding somatolactin of 232 amino acids was identified. Phylogenetic analysis showed 97% amino acid identity with White sturgeon somatolactin. RT-PCR analysis indicated that the somatolactin mRNA was only detected in pituitary. Pituitary-specific expression of the somatolactin suggested that the protein may play important physiological functions in pituitary-endocrine system of the Chinese sturgeon.

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

“…The Swiss-Prot part of the UniProt database (downloaded on 2012/02/24) was also queried. Local TBLASTX 2.2.25+ similarity searches were conducted locally against (1) 6,088 EST sequences of the genus Acipenser downloaded from NCBI-taxonomy (2011/04/18), mainly obtained from A. sinensis [39] and A. transmontanus [40] (2) a super-set of all transcripts resulting from Ensembl (release-66) including known-, novel- and pseudo-gene predictions for the following list of reference species (hereafter RS-list): Petromyzon marinus, Latimeria chalumnae, Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, Tetraodon nigroviridis and Homo sapiens. In order to identify non-coding sequences, BLASTN 2.2.25+ similarity searches were conducted locally against whole non-coding RNA gene and pseudogene sequences from Ensembl release-66 for the species of the RS-list.…”

Molecular characterization and expression pattern of dmrt1 in the immature Chinese sturgeon Acipenser sinensis

“…The complementary (c)DNAs were synthesized from 100 ng of total RNAs according to the reports described previously (Cao et al , ) using the switching mechanism at 5′ end of RNA transcript (SMART) cDNA library construction kit (Clontech; http://www.clontech.com). Briefly, 100 ng of total RNA was reverse transcribed at 42° C for 1 h in the presence of both 3′ SMART cDNA synthesis (CDS) primer A and SMART II A oligonucleotide.…”

Transcript annotation of Chinese sturgeon (Acipenser sinensis) using Iso-seq and RNA-seq data

“…As an important anadromous fish distributed in Yangtze River and Chinese coastal waters, the Chinese sturgeon (Acipenser sinensis) has a long-life span and is one of most primitive vertebrates with a history of over 200 million years 1,2 . Therefore, Chinese sturgeon is a valuable comparative model to study vertebrate evolution, physiology and immunology due to its very long evolutionary history and key phylogenetic position 3,4 . Due to dam construction, overfishing, water pollution and navigation, natural populations of Chinese sturgeon have sharply declined and there has been no spawning in the Yangtze River for eight years since 2013, resulting in extreme danger of going extinct in the wild.…”