LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly.

Background: Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity.

[Response of grain filling characteristics of maize to sowing date.].

To study the effect of different sowing dates on the process of grain filling characteristics, Jingke 528 (JK528) and Zhengdan 958 (ZD958) were used in the field experiment with two sowing dates (10th April and 14th May). The results showed that the 100-grain dry mass and yield of JK528 and ZD958 with the early spring sowing were significantly higher than that with the spring sowing date, which increased by 6.8% and 10.

[Characteristics and phylogenetic analysis of mitochondrial genome in the gobies].

The vast number of species, small size and high variation of morphology make the morphological identification and classification of gobies very difficult. In this study, the complete mitochondrial genome (mitogenome) of 26 species of gobies was analyzed, aiming at accumulating the molecular information on the identification, classification and molecular evolution of gobies. The results showed that the gene composition and arrangement of mitogenome of gobies are similar to most vertebrates.

[Effects of different accumulated temperature on photosynthetic performances of spring maize varieties during grain-filling period].

Taking cold-resistant maize variety Fengdan 3 and cold-sensitive maize variety Zhengdan 958 as test materials, field experiments were conducted in I, II, and III accumulated temperature zones in Heilongjiang Province of Northeast China to study the effects of different accumulated temperature on the photosynthetic performances of different types of cold-resistant spring maize varieties during their grain-filling period. In the three accumulated temperature zones, the tasseling and maturing periods of Fengdan 3 and Zhengdan 958 were prolonged in the order of I > II > and III, and the grain bulk density decreased in the same order. The RuBPCase and PEPCase activities of Fengdan 3 and Zhengdan 958 leaves had different temperature sensitivity.

The first complete mitochondrial genome from Bostrychus genus (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotridae fish phylogeny.

To understand the phylogenetic position of Bostrychus sinensis in Eleotridae and the phylogenetic relationships of the family, we determined the nucleotide sequence of the mitochondrial (mt) genome of Bostrychus sinensis. It is the first complete mitochondrial genome sequence of Bostrychus genus. The entire mtDNA sequence was 16508 bp in length with a standard set of 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a noncoding control region.

[Effects of PASP-KT-NAA on the grain-filling of maize in different accumulated temperature zones of Hilongjiang Province, Norheast China].

Taking the two maize varieties Zhengdan 958 and Fengdan 3 grown on the three accumulated temperature zones (I, II and III) in Heilongjiang Provice as test materials, a field investigation was made in 2010 and 2011 to study the effects of PASP-KT-NAA (PKN), a compound of exogenous plant growth regulators, on the grain filling and yield of the varieties under different environmental temperatures. From zone I to III, the air temperature at the grain filling stage had a decreasing trend, with the average minimum temperature being 12.16, 11.

Gene duplication and evidence for balancing selection acting on MHC class II DAA gene of the half-smooth tongue sole (Cynoglossus semilaevis).

Allelic polymorphism and evolution mechanism of major histocompatibility complex (MHC) genes has been investigated in many mammals, however, much less is known in teleost. In order to investigate the mechanisms creating and maintaining variability at the MHC class II DAA locus, we examined the polymorphism, gene duplication and balancing selection of MHC class II DAA gene of the half-smooth tongue sole (Cynoglossus semilaevis). We described 33 alleles in the C.

The complete mitochondrial genome of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae): genome characterization and phylogenetic considerations.

The complete mitochondrial genome sequence of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae) was determined and phylogenetic analysis was conducted to elucidate the evolutionary relationship of the marbled rockfish with other Sebastinae species. This mitochondrial genome, consisting of 17301 bp, is highly similar to that of most other vertebrates, containing the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one putative control region. Most of the genes are encoded on the H-strand, while the ND6 and seven tRNA genes (for Gln, Ala, Asn, Tyr, Ser (UCA), Glu, and Pro) are encoded on the L-strand.

Molecular cloning, characterization and expression analysis of a miiuy croaker (Miichthys miiuy) CXC chemokine gene resembling the CXCL9/CXCL10/CXCL11.

Chemokines are a large family of chemotactic cytokines playing crucial roles in the innate immune response. In the present study, we report the cloning of a CXC chemokine gene resembling the closely related CXCL9/CXCL10/CXCL11 from the miiuy croaker Miichthys miiuy (MimiCXC). Both 5'-RACE and 3'-RACE were carried out in order to obtain the complete cDNA, which consists of a 73 bp 5'-UTR, a 369 bp open reading frame encoding 122 amino acids and a 715 bp 3'-UTR.

Sequence and expression analysis of cathepsin S gene in the miiuy croaker Miichthys miiuy.

Cathepsin S (CTSS) is a lysosomal cysteine endopeptides of the papain family. In the present study, CTSS gene was isolated from miiuy croaker (Miichthys miiuy) by expressed sequence tag analysis. The complete miiuy croaker CTSS cDNA comprised 1,454 nucleotides, including 56 bp at the 5'-UTR and 394 bp at the 3'-UTR.

Molecular characterization of miiuy croaker CC chemokine gene and its expression following Vibrio anguillarum injection.

A CC chemokine gene was isolated from miiuy croaker (Miichthys miiuy) by expressed sequence tag analysis. The Mimi-CC cDNA contains an open reading frame of 429 nucleotides encoding 142 amino acid residues. The deduced Mimi-CC possesses the typical arrangement of four cysteines as found in other known CC chemokines (C³¹, C³², C⁵⁶, and C⁷⁰).

Genomic sequences comparison and differential expression of miiuy croaker MHC class I gene, after infection by Vibrio anguillarum.

Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. MHC gene family contains two main subgroups of immunologically active molecules. In order to study the molecular function and genomic characteristic of class I gene in teleost, the full lengths of MHC class Iα cDNA and genomic sequence were cloned from miiuy croaker (Miichthys miiuy).

The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciformes, Sciaenidae): structure of control region and phylogenetic considerations.

Sciaenidae is a diverse, commercially important family. To understand the phylogenetic position of Collichthys niveatus in this family, we present its complete mitochondrial genome sequence. The genome is 16469 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes.

Allelic variation, balancing selection and positive selected sites detected from MHC class Iα gene of olive flounder.

Major histocompatibility complex (MHC) genes play an important role in the immune response of vertebrates. Allelic polymorphism and pattern of evolution in MHC genes has been investigated in many mammals, however, much less is known in teleost. In the present study, we have investigated complete MHC Iα gene consists of 7 exons and 6 introns in Olive flounder (Paralichthys olivaceus).

Growth differences and differential expression analysis of pituitary adenylate cyclase activating polypeptide (PACAP) and growth hormone-releasing hormone (GHRH) between the sexes in half-smooth tongue sole Cynoglossus semilaevis.

Pituitary adenylate cyclase activating polypeptide (PACAP) and growth hormone-releasing hormone (GHRH) are regulators of growth hormone secretion. In this article, we examined the difference in growth and mRNA expression of PACAP and GHRH between the sexes in half-smooth tongue sole, an important cultured fish species indicating sexually growth dimorphism in China. Firstly, a significant body weight difference between females and males was first observed at 7 months (P<0.

Identification of immune genes of the miiuy croaker (Miichthys miiuy) by sequencing and bioinformatic analysis of ESTs.

Miiuy croaker (Miichthys miiuy) is an economically important fish in China. However, genomic research on this species is still in its infancy, and genomic resources are largely unavailable. In order to isolate functional genes involved in immunity, a normalized cDNA library was constructed from the spleen of the miiuy croaker.

Molecular cloning, genomic structure and expression analysis of major histocompatibility complex class Iα gene of half-smooth tongue sole (Cynoglossus semilaevis).

Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. The full length of MHC class Iα cDNA was cloned from half-smooth tongue sole by homology cloning and rapid amplification of cDNA ends polymerase chain reaction (RACE-PCR), genomic organization and expression of MHC Iα were examined to study the function of MHC gene in fish. The domain structure feature and antigen-binding motifs of other teleost and mammals MHC are conserved in the half-smooth tongue sole MHC Iα gene.

MHC class IIalpha gene polymorphism and its association with resistance/susceptibility to Vibrio anguillarum in Japanese flounder (Paralichthys olivaceus).

Association between polymorphism of the major histocompatibility complex (MHC) genes and disease resistance has been documented for few teleosts. In this study, we first investigate the genetic variation at the MHC IIalpha gene in Japanese flounder (Paralichthys olivaceus) for survival after challenge with bacterial infection. To explore the specific allele associated with disease resistance, about 6000 individuals from 60 families challenged with Vibrio anguillarum, which causes significantly different mortality in flounder families.

[Genomic structure of DAA gene and polymorphism within MHC-DAA alleles in Japanese flounder (Paralichthys olivaceus)].

To investigate the allele polymorphism of MHC-DAA in Japanese flounder (Paralichthys olivaceus), specific primers were designed based on the published DAA-cDNA sequence of P. olivaceus to amplify the entire introns from flounder. Gene DAA consisted of four exons and three introns.