Liqiang Zhong

Genetic diversity and population structure of yellow catfish Pelteobagrus fulvidraco from five lakes in the middle and lower reaches of the Yangtze River, China, based on mitochondrial DNA control region.

Genetic diversity and population structure of yellow catfish Pelteobagrus fulvidraco were examined by using mitochondrial DNA control region sequences in 143 specimens sampled from five lakes in the middle and lower reaches of the Yangtze River, China; 151 polymorphic sites defined 72 distinct haplotypes. Haplotype diversity indices (0.903–0.953) and nucleotide diversity indices (0.00378–0.00970) demonstrated low genetic diversity of the yellow catfish populations in the five lakes. The analysis of molecular variance and the fixation index ( = 0.0896) revealed insignificant genetic difference between samples from different lakes. In addition, neutral tests and analysis of mismatch distribution suggested that yellow catfish might have undergone a population expansion. Neighbor-joining tree indicated a correlation between these population genetic differences and geographic distance. This study revealed the extant population genetic diversity and structure of the yellow catfish and was in favor of the related fishery management issues including fishery stock identification, conservation, and artificial breeding.

Genome-wide identification, phylogeny and expressional profile of the Sox gene family in channel catfish (Ictalurus punctatus)

The Sox gene family has been systematically characterized in some fish species but not in catfish Ictalurus punctatus. In this study, 25 Sox genes were identified in the channel catfish genome and classified into seven families based on their conserved domains as follows: eight genes in SoxB group (six in SoxB1 subgroup and two in SoxB2 subgroup); five genes in SoxC group; three genes in SoxD and SoxF groups; four genes in SoxE group; and one gene in SoxH and SoxK groups. The mammalian Sox groups SoxA, G, I, and J were not present in catfish. The number of introns in channel catfish Sox genes varied from zero to 13. Sox genes were distributed unevenly across 17 chromosomes. Five members of the ancestral vertebrate Sox genes (Sox1, Sox4, Sox9, Sox11 and Sox19) experienced teleost-specific whole genome duplication during evolution, and now have two copies on different chromosomes. Expression profiles analyses indicated that the accumulation of Sox genes was associated with different tissues, and the expression pattern also differed among each Sox gene group and duplicated gene. This study constitutes a comprehensive overview of the Sox gene family in channel catfish and provides new insights into the evolution of this gene family.

New complete mitochondrial genome of the Perccottus glenii (Perciformes, Odontobutidae): additional non-coding region.

Abstract Perccottus glenii is a species of freshwater sleeper native to the Russian Far East, north-eastern China, and the northern part of the Korean Penninsula with introduced populations in other regions of Eurasia. In this study, a new complete mitochondrial genome of Perccottus glenii was reported. The circular genome is 16,510 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. Except the origin of the light strand replication (OL), an additional non-coding region was present between ND6 and tRNA-Glu in the Light strand. The overall nucleotide composition was 30.5% A, 29.2% T, 24.4% C and 15.9% G, with an A + T bias of 59.7%. The gene composition and the structural arrangement of the P. glenii complete mtDNA were identical to most of the other vertebrates. The molecular data here we presented could play a useful role to study the evolutionary relationships and population genetics of Odontobutidae fish.

Variation analysis and sample size estimation for growth indicators during PIT-tag-assisted family construction of channel catfish (Ictalurus punctatus)

Passive integrated transponder (PIT) tags can be used to overcome environmental variations caused by individual fish tanks during family selection of the channel catfish (Ictalurus punctatus), which thus permits growth comparisons among different families under identical environmental conditions. Power analysis was used to analyse variations in various growth performance measures during PIT-tag-assisted family construction of channel catfish, and this allowed sample sizes to be estimated. The experimental data suggested that, for a particular fish species, when having a low variation coefficient of fish body weight at the time of PIT marking and maintaining consistent individual sizes, the sample size required during a family growth experiment could be effectively reduced. This present study lays a theoretical foundation for analyzing variations in growth performance indicators and estimating the sample sizes during PIT-tag-assisted family construction of fish experiments.

Genetic parameters for growth and survival of the base population in channel catfish (Ictalures punctatus)

Genetic parameters were estimated for growth and pond survival of channel catfish Ictalures punctatus using full-sib and half-sib families from cultured brood females collected from five different populations of the United States.The fry and juvenile were reared,tagged,and thereafter communal-reared in one pond.Variance components and genetic parameters for growth and survival were estimated using a two traits animal model and a sire-dam threshold model.The estimated breeding values of all animals were calculated using best linear unbiased prediction.The heritability estimates for harvest body weight and harvest body length in the base population were high(0.41±0.074 and 0.32±0.064,respectively)and were significantly different from zero(P0.05).These estimates are likely biased upwards due to the common environmental effect other than additive genetic effect,although tagging body weight and tagging body length was fitted as a covariate in the mixed model to remove this effect.There was a high phenotypic and genetic correlation between harvest body weight and harvest body length(0.93 and 0.97,respectively).Heritability of pond survival was low(0.037±0.016)but still significantly different from zero(P0.05).The correlation between family breeding values for growth(harvest body weight and harvest body length)and pond survival were low(0.065 and 0.10,respectively)and not significantly different from zero(P0.05).Therefore,growth and survival must be included as breeding objective and simultaneously selected in the future generations by using a multiple trait selection index method.

Complete mitochondrial genome of paradise fish Macropodus opercularis (Perciformes: Macropodusinae)

Abstract Macropodus opercularis is a popular ornamental fish and has been widely transported around the world. In this study, the complete mitochondrial genome of M. opercularis was reported. The circular genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes, and one control region. The overall nucleotide composition was 30.9% A, 29.6% T, 24.7% C, and 14.8% G, with an A + T bias of 60.5%. The gene composition and the structural arrangement of the M. opercularis complete mtDNA were identical to most of the other vertebrates. The molecular data presented here could play a useful role in studying the evolutionary relationships and population genetics of Macropodusinae fish.

Evaluation of genetic diversity and population structure of five yellow catfish Pelteobagrus fulvidraco populations by microsatellite markers

Abstract Yellow catfish, Pelteobagrus fulvidraco, is an important commercial freshwater species in China. Knowledge about the genetic diversity of the yellow catfish is important to support the management and conservation programs, which would subsequently support the sustainable production of this species. To investigate the genetic diversity and the structure of yellow catfish in the middle and lower reaches of the Yangtze River, 125 individuals from five lakes were genotyped using 13 microsatellite markers. Moderate genetic diversity was determined in all populations, with the observed heterozygosity (HO) ranging from 0.42 to 0.49 and the expected heterozygosity (HE) ranging from 0.51 to 0.61. Low to moderate genetic differentiation among the populations was revealed from pairwise FST values (p < 0.05), as well as from analysis of molecular variance (AMOVA). The UPGMA dendrogram and Bayesian clustering analysis indicated a correlation between genetic differences and geographic distance – four populations from the lower reaches clustered together, whereas the Poyang Lake (PY) population formed a separate cluster. The present study would be helpful in the wild stock management and artificial propagation programs for yellow catfish in the middle and lower reaches of the Yangtze River.

Dynamics of the bacterial community in a channel catfish nursery pond with a cage–pond integration system

The changes in the bacterial community composition in a channel catfish nursery pond with a cage-pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage-pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

Complete mitochondrial genome of Odontobutis haifengensis (Perciformes, Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis

Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.

Complete mitochondrial genome of Chinese icefish Neosalanx tangkahkeiis (Salmoniformes, Salangidae): comparison reveals Neosalanx taihuensis not a valid name

Abstract The complete mitochondrial genome of Neosalanx tangkahkeiis was determined to be 16,550 bp in length with (A+T) content of 49.7%, and it consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the N. tangkahkeiis complete mtDNA were identical to most of other vertebrates. The sequence comparison showed that mitogenome of N. tangkahkeiis had a 99.9% of similarity with so-called N. taihuensis, indicating they are the same species and N. taihuensis is not a valid name.