Correction to: L_RNA_scaffolder: scaffolding genomes with transcripts.

Following the publication of this article [1], the authors reported that the link to the software described in the article is no longer valid.

Complete mitochondrial genome of the Siamese fighting fish (Betta splendens).

The Siamese fighting fish (Betta splendens) is one of the popular aquarium fish. Serious attentions have been paid to the biodiversity of the fish. The mitochondrial genome of the Siamese fighting fish is reported to be 17 099 bp and includes 37 genes.

Complete mitochondrial genome of the penguin tetra, Thayeria boehlkei.

The penguin tetra (Thayeria boehlkei) is one of the most popular aquarium fish and belongs to the family of Characidae. The composition, phylogeny, and classification of this family are uncertain. Here, the complete mitogenome of T.

The transcriptomes of the crucian carp complex (Carassius auratus) provide insights into the distinction between unisexual triploids and sexual diploids.

Both sexual reproduction and unisexual reproduction are adaptive strategies for species survival and evolution. Unisexual animals have originated largely by hybridization, which tends to elevate their heterozygosity. However, the extent of genetic diversity resulting from hybridization and the genomic differences that determine the type of reproduction are poorly understood.

Complete mitochondrial genome of the kissing gourami, Helostoma temminkii.

The kissing gourami (Helostoma temminkii) belongs to the Labyrinth fishes (Perciformes: Anabantoidei), which exhibits a wide variety of behavioral traits. In this study the complete mitogenome of H. temminkii was determined to be 16,740 bp in length.

L_RNA_scaffolder: scaffolding genomes with transcripts.

Background: Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments.

Complete mitochondrial genome of Chinese sleeper, Perccottus glenii.

Chinese sleeper (Perccottus glenii) belongs to the largest vertebrate order, Perciformes. In this study, the complete mitochondrial genome of P. glenii was determined to be 16,487 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes.

Primary genome scan for complex body shape-related traits in the common carp Cyprinus carpio.

To identify quantitative trait loci (QTL) that affect body shape in common carp Cyprinus carpio, a linkage map, 2159·23 cM long, was constructed with a total of 307 markers covering 51 linkage groups (LG). The map included 167 new single nucleotide polymorphism (SNP) markers derived from expressed sequence tags (EST) together with 140 microsatellite markers reported earlier. A primary genome scan was conducted for QTL for standard length (L(S)), head length (L(H)), body height (H(B)), body width (W(B)) and tail length (L(TAIL)) in an F1 line containing 92 offspring.

High throughput mining and characterization of microsatellites from common carp genome.

In order to supply sufficient microsatellite loci for high-density linkage mapping, whole genome shotgun (WGS) sequences of the common carp (Cyprinus carpio) were assembled and surveyed for microsatellite identification. A total of 79,014 microsatellites were collected which were harbored in 68,827 distinct contig sequences. These microsatellites were characterized in the common carp genome.

Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs.

Background: MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRNA regulation as well as to alter miRNA biogenesis.

Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics.

Background: Common carp (Cyprinus carpio) is one of the most important aquaculture species of Cyprinidae with an annual global production of 3.4 million tons, accounting for nearly 14% of the freshwater aquaculture production in the world. Due to the economical and ecological importance of common carp, genomic data are eagerly needed for genetic improvement purpose.

Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio).

Background: Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event.

[Genomic selection and its application].

Selective breeding is very important in agricultural production and breeding value estimation is the core of selective breeding. With the development of genetic markers, especially high throughput genotyping technology, it becomes available to estimate breeding value at genome level, i.e.

Generation of the first BAC-based physical map of the common carp genome.

Background: Common carp (Cyprinus carpio), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the all freshwater aquaculture production in the world. Apparently genomic resources are needed for this species in order to study its performance and production traits.

Molecular characterization of CART, AgRP, and MC4R genes and their expression with fasting and re-feeding in common carp (Cyprinus carpio).

Cocaine and amphetamine-regulated transcript (CART), agouti-related proteins (AgRP) and Melanocortin 4 Receptor (MC4R) involves in the control of appetite. The genes were cloned and characterized, and their regulation was studied in common carp. The CARTI and CARTII genes encode 117- and 120-amino acids, respectively.

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences.

Background: Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped.

Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio.

A bacterial artificial chromosome (BAC) library of common carp Cyprinus carpio L. was constructed as a part of ongoing common carp genome project, which is aiming assembly of common carp genome. The library, containing a total of 92,160 BAC clones with an average insert size of 141 kb, was constructed into the restriction site of Hind III on BAC vector CopyControl pCC1BAC, covering 7.

Rates and patterns of microsatellite mutations in common carp (Cyprinus carpio L.).

During genotyping 150 microsatellites in a F1 family of common carp, six mutations were found at five microsatellite loci. The overall mutation rate of common carp microsatellites was 2.53 X 10(-4) per locus per generation.

Genetic linkage mapping and analysis of muscle fiber-related QTLs in common carp (Cyprinus carpio L.).

A genetic linkage map of common carp (Cyprinus carpio L.) was constructed using Type I and Type II microsatellite markers and a pseudo-testcross mapping strategy. The microsatellite markers were isolated from microsatellite-enriched genomic libraries and tested for their segregation in a full-sib mapping panel containing 92 individuals.