BackgroundThe yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited.Methodology and principal findingsIllumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp. A total of 9093 unigenes showed significant similarities to known proteins in public databases: 4477 and 6391 of B. yarrelli unigenes were mapped to the Gene Ontology (GO) and Clusters of Orthologous Groups (COG) databases, respectively. Moreover, 9635 unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In addition, 8568 microsatellites (simple sequence repeats, SSRs) were detected, and 31 pairs of polymorphic primers were characterized using wild populations of B. yarrelli from the Nujiang River, Yunnan Province, China.Conclusion/SignificanceThese sequences enrich the genomic resources for B. yarrelli and will benefit future investigations into the evolutionary and biological processes of this and related Bagarius species. The SSR markers developed in this study will facilitate construction of genetic maps, investigations of genetic structures and germplasm polymorphism assessments in B. yarrelli.

The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the “duplicated MIR482” evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the “frameshift targeted mechanism” to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

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This study examined genetic variation in the major histocompatibility complex (MHC) Class II B gene in turbot (Scophthalmus maximus) by virulent bacterial pathogen challenge. One hundred fry from each of six families were infected with Edwardsiella tarda by intraperitoneal injection. Family mortality ranged from 28.0% to 83.3%. Complete exon 2 and intron 1 sequences of MHC Class II B genes were amplified from five survivor and five non-survivor individuals per family using the clone-sequence method. Thirty-seven sequences from 60 individuals revealed 37 different alleles, 25 of which were unique to this study. The 25 unique alleles belonged to 16 major allele types. Nine alleles were used to examine the association between alleles and resistance/susceptibility to disease. Five alleles were present in an individual, suggesting a minimum of three loci or copies of the turbot MHC Class II B gene. The rate of non-synonymous substitution (d N ) was 2.30 and 1.58 times higher than synonymous substitution (d S ) in the peptide-binding regions (PBR) and non-PBR in whole families, respectively, which suggested balancing selection on exon 2 of the MHC Class II B gene in turbot. One allele, Scma-DBB1*02, was significantly more prevalent in survivor stock than in non-survivor stock (P=0.001). Therefore, this allele might be associated with resistance to bacteria. A second allele, Scma-DBB1*10, was significantly more prevalent in non-survivor stock (P=0.021), and is likely associated with susceptibility to bacteria. turbot (Scophthalmus maximus), Edwardsiella tarda, major histocompatibility complex II B, polymorphism, resistance, susceptibility

ABSTRACT. To study the phylogenetic relationships of the genus Gymnothorax (moray eels) distributed in South China Sea, polymerase chain reactions were performed, and the amplification products were sequenced by cloning into the PMD18T-vector (TaKaRa). The entire gene sequences encoding cytochrome b (1140 bp) for 16 Gymnothorax