Project description:Chanodichthys erythropterus is a fierce carnivorous fish widely found in East Asian waters. It is not only a popular food fish in China, it is also a representative victim of overfishing. Genetic breeding programs launched to meet market demands urgently require high-quality genomes to facilitate genomic selection and genetic research. In this study, we constructed a chromosome-level reference genome of C. erythropterus by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. The 1.085 Gb C. erythropterus genome was assembled from 132 Gb of Nanopore sequence. The assembled genome represents 98.5% completeness (BUSCO) with a contig N50 length of 23.29 Mb. The contigs were clustered and ordered onto 24 chromosomes covering roughly 99.49% of the genome assembly with Hi-C data. Additionally, 33,041 (98.0%) genes were functionally annotated from a total of 33,706 predicted protein-coding sequences by combining transcriptome data from seven tissues. This high-quality assembled genome will be a precious resource for future molecular breeding and functional genomics research of C. erythropterus.
Project description:Melanocortin-4 receptor (MC4R) plays important roles in regulation of multiple physiological processes, and interaction of MC4R and melanocortin receptor accessory protein 2 (MRAP2) is suggested to play pivotal role in energy balance of vertebrates. Topmouth culter (Culter alburnus) is an economically important freshwater fish in China. Herein we cloned culter mc4r, mrap2a, and mrap2b. Culter mc4r consisted of a 981 bp open reading frame encoding a protein of 326 amino acids. qRT-PCR revealed that mc4r, mrap2a, and mrap2b were primarily expressed in the central nervous system. In the periphery, mc4r and mrap2b were expressed more widely in the male, while mrap2a was expressed more widely in the female. Culter MC4R could bind to four peptide agonists and increase intracellular cAMP production dose dependently. Culter MC4R was constitutively active in both cAMP and ERK1/2 pathways, which was differentially regulated by culter MRAP2a and MRAP2b. Culter MRAP2a significantly increased Bmax and decreased agonist-stimulated cAMP, while MRAP2b increased cell surface and total expression but did not affect Bmax and agonist-stimulated cAMP. These results will aid the investigation of the potential physiological processes that MC4R might be involved in topmouth culter.
Project description:Oryzias sinensis, also known as Chinese medaka or Chinese ricefish, is a commonly used animal model for aquatic environmental assessment in the wild as well as gene function validation or toxicology research in the lab. Here, a high-quality chromosome-level genome assembly of O. sinensis was generated using single-tube long fragment read (stLFR) reads, Nanopore long-reads, and Hi-C sequencing data. The genome is 796.58 Mb, and a total of 712.17 Mb of the assembled sequences were anchored to 23 pseudo-chromosomes. A final set of 22,461 genes were annotated, with 98.67% being functionally annotated. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of genome assembly and gene annotation reached 95.1% (93.3% single-copy) and 94.6% (91.7% single-copy), respectively. Furthermore, we also use ATAC-seq to uncover chromosome transposase-accessibility as well as related genome area function enrichment for Oryzias sinensis. This study offers a new improved foundation for future genomics research in Chinese medaka.
Project description:Kmeria septentrionalis is a critically endangered tree endemic to Guangxi, China, and is listed on the International Union for Conservation of Nature's Red List. The lack of genetic information and high-quality genome data has hindered conservation efforts and studies on this species. In this study, we present a chromosome-level genome assembly of K. septentrionalis. The genome was initially assembled to be 2.57 Gb, with a contig N50 of 11.93 Mb. Hi-C guided genome assembly allowed us to anchor 98.83% of the total length of the initial contigs onto 19 pseudochromosomes, resulting in a scaffold N50 of 135.08 Mb. The final chromosome-level genome, spaning 2.54 Gb, achieved a BUSCO completeness of 98.9% and contained 1.67 Gb repetitive elements and 35,927 coding genes. This high-quality genome assembly provides a valuable resource for understanding the genetic basis of conservation-related traits and biological properties of this endangered tree species. Furthermore, it lays a critical foundation for evolutionary studies within the Magnoliaceae family.
Project description:The mulberry looper (Phthonandria atrilineata), a geometrid moth, plays a pivotal role in the destruction of mulberry trees (Morus spp.). In China, P. atrilineata is the most significant insect pest to sericulture, as it feeds on mulberry leaves and spreads diseases. The outbreak trend of P. atrilineata has been expanding yearly, causing substantial economic losses. Despite its ecological and economic importance, knowledge about the genomic background of P. atrilineata remains limited. Here, we report a chromosome-level reference genome of P. atrilineata, with a total size of 336.55 Mb, containing 15,026 protein-coding genes and 39.72% repeat sequences. These findings have the potential to shed light on the genetic basis of the destructive nature and environmental adaptation of P. atrilineata, offering valuable genomic resources for understanding genome evolution and pest management within this Lepidopteran pest.
Project description:Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.
Project description:Chromosome-scale assembly and QTL mapping for major economic traits of Culter alburnus L. genome using Illumina, PacBio sequencing with Hi-C mapping information