Chuanju Dong

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250u2009K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94u2009cM with an average locus interval of 0.75u2009cM and an average marker interval of 0.38u2009cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357u2009Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.

Complete mitochondrial genome of Sarcocheilichthys parvus (Cypriniformes, Cyprinidae)

Abstract In this study, we sequenced and characterized the complete mitochondrial genome of Sarcocheilichthys lacustris from Heilongjiang River (Amur River) at fuyuan county, Heilongjiang province, China. The circular mitochondrial genome of S. lacustris was determined to be 16,684u2009bp in length. It contains typical complement of 13 protein coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 control region.

Complete mitochondrial genome ofSarcocheilichthys lacustris(Cypriniformes, Cyprinidae)

The complete mitochondrial genome of Sarcocheilichthys parvus was first obtained. The genome is 16,677 bp in length with 56.36% A+T content, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 noncoding control region. It has the typical vertebrate mitochondrial gene arrangement.

Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake

BackgroundAmur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, providing us a valuable material to understand the adaptation mechanism against extreme environmental stress in teleost.ResultsIn this study, we generated high-throughput RNA-Seq data from three tissues gill, liver and kidney of L. waleckii living in the soda lake Dali Nor and the fresh water lake Ganggeng Nor, then performed parallel comparisons of three tissues. Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions. We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01and fold-change ≥ 2. Further analysis revealed that well-known functional categories of genes and signaling pathway, which are associated with stress response and extreme environment adaptation, have been significantly enriched, including the functional categories of “response to stimulus”, “transferase activity”, “transporter activity” and “oxidoreductase activity”, and signaling pathways of “mTOR signaling”, “EIF2 signaling”, “superpathway of cholesterol biosynthesis”. We also identified significantly DEGs encoding important modulators on stress adaptation and tolerance, including carbonic anhydrases, heat shock proteins, superoxide dismutase, glutathione S-transferases, aminopeptidase N, and aminotransferases.ConclusionsOverall, this study demonstrated that transcriptome changes in L. waleckii played a role in adaptation to complicated environmental stress in the highly alkalized Dali Nor lake. The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.

Effect of solution treatment on the fatigue behavior of an as-forged Mg-Zn-Y-Zr alloy.

Through investigating and comparing the fatigue behavior of an as-forged Mg-6.7Zn-1.3Y-0.6Zr (wt.%) alloy before and after solid solution treatment (T4) in laboratory air, the effect of T4 treatment on fatigue crack initiation was disclosed. S-N curves illustrated that the fatigue strength of as-forged samples was 110u2009MPa, whereas the fatigue strength of T4 samples was only 80u2009MPa. Observations to fracture surfaces demonstrated that for as-forged samples, fatigue crack initiation sites were covered with a layer of oxide film. However, due to the coarse grain structure and the dissolution of MgZn2 precipitates, the activation and accumulation of {10–12} twins in T4 samples were much easier, resulting in the preferential fatigue crack initiation at cracked twin boundaries (TBs). Surface characterization demonstrated that TB cracking was mainly ascribed to the incompatible plastic deformation in the twinned area and nearby α-Mg matrix.

Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment

The Amur ide (Leuciscus waleckii) is a cyprinid fish that is widely distributed in Northeast Asia. The Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50u2009mmol/L (pH 9.6), thus providing an exceptional model with which to characterize the mechanisms of genomic evolution underlying adaptation to extreme environments. Here, we developed the reference genome assembly for L. waleckii from Lake Dali Nur. Intriguingly, we identified unusual expanded long terminal repeats (LTRs) with higher nucleotide substitution rates than in many other teleosts, suggesting their more recent insertion into the L. waleckii genome. We also identified expansions in genes encoding egg coat proteins and natriuretic peptide receptors, possibly underlying the adaptation to extreme environmental stress. We further sequenced the genomes of 10 additional individuals from freshwater and 18 from Lake Dali Nur populations, and we detected a total of 7.6 million SNPs from both populations. In a genome scan and comparison of these two populations, we identified a set of genomic regions under selective sweeps that harbor genes involved in ion homoeostasis, acid-base regulation, unfolded protein response, reactive oxygen species elimination, and urea excretion. Our findings provide comprehensive insight into the genomic mechanisms of teleost fish that underlie their adaptation to extreme alkaline environments.

Genome-wide identification, phylogeny, and expression of fibroblast growth genes in common carp

Fibroblast growth factors (FGFs) are a large family of polypeptide growth factors, which are found in organisms ranging from nematodes to humans. In vertebrates, a number of FGFs have been shown to play important roles in developing embryos and adult organisms. Among the vertebrate species, FGFs are highly conserved in both gene structure and amino-acid sequence. However, studies on teleost FGFs are mainly limited to model species, hence we investigated FGFs in the common carp genome. We identified 35 FGFs in the common carp genome. Phylogenetic analysis revealed that most of the FGFs are highly conserved, though recent gene duplication and gene losses do exist. By examining the copy number of FGFs in several vertebrate genomes, we found that eight FGFs in common carp have undergone gene duplications, including FGF6a, FGF6b, FGF7, FGF8b, FGF10a, FGF11b, FGF13a, and FGF18b. The expression patterns of all FGFs were examined in various tissues, including the blood, brain, gill, heart, intestine, muscle, skin, spleen and kidney, showing that most of the FGFs were ubiquitously expressed, indicating their critical role in common carp. To some extent, examination of gene families with detailed phylogenetic or orthology analysis verified the authenticity and accuracy of assembly and annotation of the recently published common carp whole genome sequences. Gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp FGF gene family provides an important genomic resource for future biochemical, physiological, and phylogenetic studies on FGFs in teleosts.

Genome wide identification of scavenger receptors class A in common carp (Cyprinus carpio) and their expression following Aeromonas hydrophila infection

Scavenger receptors class A (SCARAs) is a subgroup of diverse families of pattern recognition receptors that bind a range of ligands, and play important roles in innate immune processes through pathogens detection, adhesion, endocytosis, and phagocytosis. However, most studies of SCARAs have focused on mammals, and much less is known of SCARAs in fish species. In this study, we identified 7 SCARAs across the common carp genome, which were classified into four subclasses according to comparative genomic analysis including sequence similarities analysis, gene structure and functional domain prediction. Further phylogenetic and syntenic analysis supported their annotation and orthologies. Through examining gene copy number of SCARA genes across several vertebrates, SCARA2, SCARA3 and SCARA4 were found have undergone gene duplication. The expression patterns of SCARAs in common carp were examined during early developmental stages, in healthy tissues, and after Aeromonas hydrophila infection. Most SCARA genes were ubiquitously expressed during common carp early developmental stages, and presented diverse patterns in various healthy tissues, with relatively high expression levels in spleen, liver, intestine, gill and brain, indicating their critical roles likely in maintaining homeostasis and host immune response activities. After A. hydrophila infection, most SCARA genes were up-regulated at 4xa0h post infection in mucosal tissue intestine, while generally up-regulated at 12xa0h post infection in spleen, suggesting a tissue-specific pattern of regulation. Taken together, all these results suggested that SCARA genes played important roles in host immune response to A. hydrophila infection in common carp, and provided important genomic resources for future studies on fish disease management.

Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes

Common carp (Cyprinus carpio L.) is one of the oldest, most widely farmed commercially important freshwater fish in the world. However, many undetermined phylogenetic relationships and origins of common carp lineages remain, which are obstacles to conservation and genetic breeding of this species. Phylogenetic analyses based on molecular tools are helpful to distinguish the origin of species, understand and clarify their evolutionary history, and provide a genetic basis for selective breeding. In this study, we demonstrated a method to extract complete mitochondrial genome sequences from whole-genome resequencing data using the Illumina platform. The complete mitochondrial genome sequences of 26 individuals representing nine strains were obtained and subjected to a phylogenetic analysis. We reconstructed the phylogenetic topologies of the nine strains and analyzed the haplotypes. Results from both analyses suggested that the genome sequences belonged to two distinct subspecies from Europe and East Asia. We also estimated the time of divergence of the nine strains, which was up to 100 KYA. The phylogenetic results clarified the breeding history of Songpu mirror carp and suggest that this species may be hybrid of paternal European mirror carp and maternal Xingguo red carp. The results also support a previous hypothesis that koi may have originated from or have close ancestry with Oujiang color carp in China.

Phylogenetic and Evolutionary Analyses of the Frizzled Gene Family in Common Carp (Cyprinus carpio) Provide Insights into Gene Expansion from Whole-Genome Duplications

In humans, the frizzled (FZD) gene family encodes 10 homologous proteins that commonly localize to the plasma membrane. Besides being associated with three main signaling pathways for cell development, most FZDs have different physiological effects and are major determinants in the development process of vertebrates and. Here, we identified and annotated the FZD genes in the whole-genome of common carp (Cyprinus carpio), a teleost fish, and determined their phylogenetic relationships to FZDs in other vertebrates. Our analyses revealed extensive gene duplications in the common carp that have led to the 26 FZD genes that we detected in the common carp genome. All 26 FZD genes were assigned orthology to the 10 FZD genes of on-land vertebrates, with none of genes being specific to the fish lineage. We postulated that the expansion of the FZD gene family in common carp was the result of an additional whole genome duplication event and that the FZD gene family in other teleosts has been lost in their evolution history with the reason that the functions of genes are redundant and conservation. Through the expression profiling of FZD genes in common carp, we speculate that the ancestral gene was likely capable of performing all functions and was expressed broadly, while some descendant duplicate genes only performed partial functions and were specifically expressed at certain stages of development.