Genome Evolutionary Studies Research Articles

Construction of a high-density linkage map and QTL detection of growth and sex in blotched snakehead (Channa maculata)

High-density genetic linkage maps are comprehensively used in quantitative trait loci (QTLs) mapping, trait-related genes identification, marker-assisted selection, genome assembly and comparative genomic analysis in domestic species. The blotched snakehead (Channa maculata) is an important aquaculture species in China and Southeast Asia, but the genetic improvement was lagged by lacking of genomic information. In this study, the first high-density genetic linkage map was constructed for blotched snakehead using 2b-RAD sequencing technology. The consensus map consists of 6352 single nucleotide polymorphism (SNP) markers that are assigned to 21 linkage groups (LGs) and spanning 2143.7 cM with an average marker interval of 0.34 cM. Comparative genomic analysis revealed 1:1 and/or 1:2 syntenic relationships between blotched snakehead LGs and chromosomes of medaka, European seabass and northern snakehead separately. Nine chromosome-wide QTLs associated with body weight were identified in three LGs, explaining 9.8–11.9% of the phenotypic variation. Putative candidate genes for growth rate, such as bone morphogenetic protein 6 (BMP 6), were identified adjacent to the QTLs. A single major locus tightly linked to sex was identified in LG2 that explained 98.8–100% of the phenotypic variation.Four markers within the sex-linked locus were found to be heterogametic in males and homogametic in females. One sex-specific SNP marker located in the sex QTL region was validated for practical verification of sex in blotched snakehead. Those results suggest that the LG2 may be a sex-related chromosome in blotched snakehead and an XX/XY chromosomal sex determination system in this species. The high-density linkage map and QTLs supply a basis for genome evolutionary studies, QTL fine mapping of economic traits and sex-control breeding in blotched snakehead.

High-density genetic linkage map and QTL fine mapping of growth and sex in snakehead (Channa argus)

High-density genetic linkage maps are essential for quantitative trait locus (QTL) mapping, candidate gene identification, marker-assisted selection, genome assembly and comparative genomic analysis in aquaculture species. Snakehead (Channa argus) is an important aquaculture species in China, but the genetic improvement of this species is still in its infancy. In this study, a high-density genetic linkage map was constructed for snakehead using 2b-RAD sequencing technology. The consensus map contains 3151 single nucleotide polymorphism (SNP) markers assigned to 24 linkage groups (LGs) and spanning 2728.9 cM with an average marker interval of 0.87 cM. Comparative genomics revealed a 1:1 syntenic relationship between snakehead LGs and chromosomes of medaka and European seabass. Fourteen chromosome-wide QTLs associated with body weight and body length were identified in five LGs, explaining 9.6–12.8% of the phenotypic variation. Potential candidate growth-related genes, such as SATB homeobox 2 (satb2), were identified within the QTL intervals. A single major locus for sex determination was identified in LG5 that explained 97.4–100% of the phenotypic variation. Six markers with a sex-determining locus were found to be heterogametic in males and homogametic in females. A sex-specific SNP marker located in the sex QTL region was validated for practical verification of sex in snakehead. All of the results suggest an XX/XY sex determination system in this species. This high-density genetic map and QTL analysis supply a basis for genome evolutionary studies, genome assembly and QTL fine mapping of complex traits in snakehead.

Characterization of some satellite DNA families in Deschampsia antarctica (Poaceae)

Deschampsia antactica E. Desv. is one of the only two native vascular plants of Antarctica, having a disjunct distribution with South America. Its presence in different environmental conditions turns it into an interesting evolution model, particularly for genomic evolutionary studies. The repetitive DNA is a genome component that cause important changes in genome size and chromosome organization, and therefore, its variation is very important in group’s delimitation. Some tandem repetitive DNA sequences, known as satellite DNA (satDNAs) are shared between many groups of Poaceae (e.g., of these are the CON1, CON2, COM1, and COM2 sequences) highlighting its evolutionary component. This study aims to identify, classify, and characterize repetitive elements in the D. antarctica genome by clustering analysis of genome sequences, focusing on the CON1, CON2, COM1, and COM2. Repetitive DNA represented about 73.3% of the D. antarctica genome. All studied populations presented loci for the studied satDNAs but the distribution pattern showed differences that seem to be related to the geographic distribution. The analysis of CON/COM sequences in D. antarctica contributes to the understanding of these elements in Poaceae genomes and highlights the importance of changes in chromosome organization of repetitive DNA in populations with fragmented geographical distribution. The distribution of such chromosome changes may both reflect the process of colonization of D. antarctica in Antarctica and explain some evolutionary processes of differentiation in Deschampsia species complex in the Patagonia, which is still unresolved with other DNA sequences.

A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (Carassius auratus) Using 2b-RAD Sequencing.

A high-resolution genetic linkage map is essential for a wide range of genetics and genomics studies such as comparative genomics analysis and QTL fine mapping. Crucian carp (Carassius auratus) is widely distributed in Eurasia, and is an important aquaculture fish worldwide. In this study, a high-density genetic linkage map was constructed for crucian carp using 2b-RAD technology. The consensus map contains 8487 SNP markers, assigning to 50 linkage groups (LGs) and spanning 3762.88 cM, with an average marker interval of 0.44 cM and genome coverage of 98.8%. The female map had 4410 SNPs, and spanned 3500.42 cM (0.79 cM/marker), while the male map had 4625 SNPs and spanned 3346.33 cM (0.72 cM/marker). The average recombination ratio of female to male was 2.13:1, and significant male-biased recombination suppressions were observed in LG47 and LG49. Comparative genomics analysis revealed a clear 2:1 syntenic relationship between crucian carp LGs and chromosomes of zebrafish and grass carp, and a 1:1 correspondence, but extensive chromosomal rearrangement, between crucian carp and common carp, providing evidence that crucian carp has experienced a fourth round of whole genome duplication (4R-WGD). Eight chromosome-wide QTL for body weight at 2 months after hatch were detected on five LGs, explaining 10.1–13.2% of the phenotypic variations. Potential candidate growth-related genes, such as an EGF-like domain and TGF-β, were identified within the QTL intervals. This high-density genetic map and QTL analysis supplies a basis for genome evolutionary studies in cyprinid fishes, genome assembly, and QTL fine mapping for complex traits in crucian carp.

Genome wide identification, phylogeny, and expression of bone morphogenetic protein genes in tetraploidized common carp (Cyprinus carpio)

Bone morphogenetic proteins (Bmps) are a group of signaling molecules known to play important roles during formation and maintenance of various organs, not only bone, but also muscle, blood and so on. Common carp (Cyprinus carpio) is one of the most intensively studied fish due to its economic and environmental importance. Besides, common carp has encountered an additional round of whole genome duplication (WGD) compared with many closely related diploid teleost, which make it one of the most important models for genome evolutionary studies in teleost. Comprehensive genome resources of common carp have been developed recently, which facilitate the thorough characterization of bmp gene family in the tetraploidized common carp genome. We identified a total of 44 bmps from the common carp genome, which are twice as many as that of zebrafish. Phylogenetic analysis revealed that most of bmps are highly conserved. Comparative analysis was performed across six typical vertebrate genomes. It appeared that all the bmp genes in common carp were duplicated. Obviously, the expansion of the bmp gene family in common carp was due to the latest additional round of whole genome duplication and made it more abundant than other diploid teleosts. Expression signatures were assessed in major tissues, including gill, intestine, liver, spleen, skin, heart, gonad, muscle, kidney, head kidney, brain and blood, which demonstrated the comprehensive expression profiles of bmp genes in the tetraploidized genome. Significant gene expression divergences were observed which revealed substantial functional divergences of those duplicated bmp genes post the latest WGD event. The conserved synteny blocks of bmp5s revealed the genome rearrangement of common carp post the 4R WGD. The whole set of bmp gene family in common carp provides insight into gene fate of tetraploidized common carp genome post recent WGD.

Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea).

BackgroundComparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012).ResultsWe present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure.ConclusionsNext-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-566) contains supplementary material, which is available to authorized users.

Complete nucleotide sequence of the Cryptomeria japonicaD. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

BackgroundThe recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.ResultsThe C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements.ConclusionThe observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.

Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning.

Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning.