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.

The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family.

A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.

Mitochondrial DNA sequence of Culter compressocorpus.

In this study, the complete mitochondrial genome of Culter compressocorpus was detected and annotated. The circular mtDNA molecule was 16,623 bp in length which contains 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and the non-coding control region (D-loop). Its total protein-coding genes content is 68.67% in whole mitochondrial genome. The mitochondrial genome can contribute to the studies on geographical distribution and genetic diversity of C. compressocorpus resources, as well as molecular phylogeny and species identification in Cyprinidae.

Mitochondrial DNA sequence of Pseudorasbora parva (Cyprinidae: Gobioninae).

In this study, the complete mitochondrial genome of Pseudorasbora parva (Cyprinidae: Gobioninae) was determined. The circular mtDNA molecule was 16,601 bp in length which contains 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes and non-coding control region (D-loop). The critical central conserved sequences were also detected. Its total A + T content is 55.97%. The mitochondrial genome can contribute to the studies on geographical distribution and genetic diversity of P. parva resources, as well as molecular phylogeny and species identification in Cyprinidae.

The complete mitochondrial genome sequence of Hemiculter leucisculus.

The complete mitochondrial genome of Hemiculter leucisculus was determined to be 16,617 bp. It contains the structure of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and non-coding control region (D-loop). The critical central conserved sequences (CSB-D, CSB-E, and CSB-F) were also detected. The determination of H. leucisculus mitogenome would play an important role in genetic diversity and population vitality in Cyprinidae.

The complete mitochondrial genome sequence of white-spotted char (Salvelinus leucomaenis).

The complete sequence of the mitochondrial genome of the white-spotted char (Salvelinus leucomaenis) was determined to be 16,658 bp in length, which contains the control region (CR), the origin of light-strand replication (OL), 22 transfer RNA genes, 2 ribosomal genes and 13 protein-coding genes. Overall, base composition of the complete mitochondrial DNA was 28.20% A, 26.51% T, 28.39% C, 16.90% G, with 54.71% AT.

Complete mitochondrial genome sequence of Romanogobio tenuicorpus (Amur whitefin gudgeon).

Amur whitefin gudgeon (Romanogobio tenuicorpus) belongs to the family Cyprinidae, it is freshwater aquaculture species in China. In the report, we determined the complete mitochondrial genome sequence of Romanogobio tenuicorpus, which is 16,600 bp long circular molecule with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, the conserved sequence blocks, CSB1, CSB2 and CSB3 were also detected.

The Complete mitochondrial genome of Spinibarbus denticulatus (Oshima).

Spinibarbus denticulatus (Oshima) is a rare and commercial fish. The complete mitochondrial genome sequence of S. denticulatus will help us to study the genetic of conversation, such as the genetic diversity and genetic structure, and provides the basis for the study in evolution. In this paper, the complete mitochondrial genome of S. denticulatus was determined to be 16,549 bp in length by Sanger sequencing technology. Thirteen protein-coding genes, 22 tRNA genes and 2 ribosomal genes were characterized. We also analyzed the structure of control region, 6 CSBs (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E and CSB-F) and 1 TAS were identified, the control region also included an AT unit tandem repeat with 17 repeat times.

Mitochondrial DNA sequence of Mongolian redfin (Chanodichthys mongolicus).

Monglian redfin is a kind of freshwater aquaculture species which has an important economic value in China. In this study, we report the complete sequence of mitochondrial genome of Monglian redfin. The complete mitochondrial genome sequence is determined to be 16,621 base pairs (bp) in length and contain 13 protein-coding gene (PCGs), 22 transfer RNA genes, large (rrnL) and small (rrnS) ribosomal RNA, and the non-coding control region. Its total A+T content is 55.98%. We also analyzed the structure of control region, six conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E and CSB-F) and one potential termination-associated sequence were detected and the control region also included a 2-bp tandem repeat with eight repeat times.

[Effects of delayed first feeding on growth and survival of Hucho taimen larvae].

This paper studied the effects of delaying first breeding Hucho taimen larvae for different days on the larvae growth, survival, and body size. Five treatments were installed, i. e. , feeding begins on the first eating day (control, S0) and on the 9th, 12th, 15th, and 18th days after the first eating day (S1 -S4) at 10.4-14.9 degree C, respectively. By the end of the experiment (36-day), the growth rate and initial feeding rate in S1 was higher than that in S0, and the overall mortality rate in S1 was lower, but the body size and mass in S1and S0 had no significant difference. Compared with S0, S2 had higher growth rate, initial feeding rate, total mortality, and self-mutilation mortality, the body mass was significantly lower, but the body size had less difference. S3 had higher first feeding rate, body size, total mortality, and self-mutilation mortality, but significantly lower body mass than S0, whereas the growth rate had less difference. In S4, the growth rate and body mass were lower, and the total mortality and self-mutilation mortality were higher than those in S0. It was suggested that under the same conditions, delaying first feeding for 9 days would induce H. taimen larvae presenting "completely compensatory growth", and this feeding way could be applied for the culture of H. taimen larvae in their initial feeding period.

[Optimal feeding strategy for juvenile Hucho taimen].

Three experiments including starvation and re-feeding, starvation and re-feeding recovery, and feeding frequency per day were conducted to approach the optimal feeding strategy for the growth and survival of juvenile Hucho taimen. In the experiment of starvation and re-feeding, all groups of restricted feeding showed non-compensatory growth. However, in the experiment of starvation and re-feeding recovery, different degrees of compensatory growth appeared in different starving groups, among which, the half a day starvation and half a day feeding group (S1/2) had a weight increment approximately the same as the control, and showed completely compensatory growth, indicating that the S1/2 could be a useful feeding strategy for the juvenile H. taimen at its early growth stage with the body mass from 0 to 2 g and at the water temperature from 9 to 15.3 degrees C. In feeding frequency experiment, the group T3 (three meals per day) had the highest body length, body mass, specific growth rate, and relatively high food conversion ratio, indicating that three meals a day could be more effective for improving the growth performance of juvenile H. taimen at its late stage with the body mass from 2 to 21 g and at the water temperature from 8.8 to 15.5 degrees C.

[Analysis of genetic diversity on 9 wild stocks of taimen (Hucho taimen) by microsatellite markers].

Taimen (Hucho taimen) is a native fish species in China and it is in the state of endangerment. To explain clearly the genetic diversity and genetic structure, 9 wild populations of taimen were investigated using 20 microsatellite markers. The results showed that their observed heterozygosity ranged from 0.0994 to 0.8882, the expected heterozygosity varied from 0.2005 to 0.8759, and the range of PIC index was from 0.3432 to 0.5261 while population from Huma River had low genetic diversity. Fst of matching group ranged from 0.0246 to 0.2333 (P <0.0001)and Nm varied among 0.8216 to 9.9292, which indicated that the genetic differentiation was remarkable among populations.The half/full-sib family tests detected a proportion of half/full-sib family groups varying among 27.78% to 90.91%, showing a high inbred pressure and a risk of bottlenecks experienced by most groups. The AMOVA results showed that the global Fst was 0.1081; the clustering result showed that individuals from Beiji tributary of Heilongjiang River clustered as one clade, all individuals from Huma River and Wusuli River clustered as one clade and all individuals from the upper reaches of the Heilongjiang River clustered as another clade. All these results indicated that the decrease of taimen resource has affected the gene exchange among their populations. In order to achieve full protection of taimen germplasm resources, we should put an end to the destructive fishing for taimen and promotegene exchange among their populations.

[Applicability of microsatellite DNA markers to the parental identification of Hucho taimen (Pallas)].

Using seven pairs of microsatellite markers we studied the relationship between the size of the the candidate groups and the microsatellite paternity testing accuracy by separate breed or the microsatellite paternity appraisal ability by mixed breed. By computer software analysis, the appraisal ability decreased with the candidate groups increase. For the 81 putative parents the microsatellite paternity testing accuracy was 80% and the microsatellite paternity appraisal ability was 78.9%; for the 9 putative parents, the testing accuracy was 93.3% and the appraisal ability was 92.2%. The results indicated that the microsatellite DNA markers can be used for the parentage determination of Hucho taimen Pallas.