A5014074729- Aquaculture disease management and microbiota
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genomics and Phylogenetic Studies
- Immune Response and Inflammation
- Chromosomal and Genetic Variations
- Animal Genetics and Reproduction
- Cancer-related molecular mechanisms research
- Reproductive biology and impacts on aquatic species
- interferon and immune responses
- Genetic diversity and population structure
- Identification and Quantification in Food
- MicroRNA in disease regulation
- Invertebrate Immune Response Mechanisms
- Plant and Fungal Interactions Research
- Fish Biology and Ecology Studies
- RNA modifications and cancer
- Vibrio bacteria research studies
- Physiological and biochemical adaptations
- Fish Ecology and Management Studies
- Plant Pathogenic Bacteria Studies
- Protist diversity and phylogeny
- NF-κB Signaling Pathways
- Robotics and Automated Systems
- Kruppel-like factors research
- Fractal and DNA sequence analysis
Chinese Academy of Fishery Sciences
2019-2023
Marine Biology Institute of Shandong Province
2022-2023
Qingdao National Laboratory for Marine Science and Technology
2019-2023
Jilin Agricultural University
2023
Laoshan Laboratory
2023
Ministry of Agriculture and Rural Affairs
2022
Huazhong Agricultural University
2012-2019
Ministère de l'Agriculture et de la Souveraineté alimentaire
2019
Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a inbred) and mexicana are assembled using a meta-assembly strategy after sequencing 10 lines derived maize-teosinte cross. Comparative analyses reveal high level diversity between Mo17, B73, including three Mb-size structural rearrangements. The spontaneous mutation rate estimated be 2.17 × 10-8...
Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions lincRNAs responses rice to phosphate (Pi) starvation has not been performed. Here, we used computational method predict Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from roots shoots control A competing endogenous (ceRNA) network was constructed for each tissue by considering...
Competing endogenous RNAs (ceRNAs) are vital regulators of gene networks in mammals. The involvement noncoding (ncRNAs) as ceRNA genotypic sex determination (GSD) and environmental (ESD) fish is unknown. Chinese tongue sole, which has both GSD ESD mechanisms, was used to map the dynamic expression pattern ncRNAs mRNA gonads during differentiation. Transcript patterns shift differentiation phase, modulation occurs through crosstalk differentially expressed long (lncRNAs), circular (circRNAs),...
Abstract Background The deer antler, a remarkable mammalian appendage, has growth rate surpassing that of any other known osseous organ. Emerging evidence indicates circRNA and MAPK1 play critical roles in chondrocytes. Thus, exploration their functions antler chondrocytes will help us to understand the mechanism regulating rapid growth. Methods qRT-PCR, western blot, immunohistochemistry were used assess expression mRNAs proteins. CCK-8, EdU, Cell migration, ALP activity detection, staining...
Long intergenic non-coding RNAs (lincRNAs) play important roles in various biological processes plants. However, little information is known about the evolutionary characteristics of lincRNAs among closely related plant species. Here, we present a large-scale comparative study lincRNA transcription patterns nine citrus By strand-specific RNA-sequencing, identified 18 075 (14 575 loci) from 34 tissue samples. The results indicated that evolution more rapid than mRNAs. In total, 82.8-97.6%...
Heat shock proteins 70 (HSP70s) are known to play essential roles in organisms' response mechanisms various environmental stresses. However, no systematic identification and functional analysis has been conducted for HSP70s the turbot (Scophthalmus maximus), a commercially important worldwide flatfish. Herein, 16 HSP70 genes unevenly distributed on nine chromosomes were identified at genome-wide level. Analyses of gene structure, motif composition, phylogenetic relationships provided...
Vibrio harveyi is a major bacterial pathogen that causes fatal vibriosis in Chinese tongue sole (Cynoglossus semilaevis), resulting massive mortality the farming industry. However, molecular mechanisms of C. semilaevis response to V. infection are poorly understood. Here, we performed transcriptomic analysis semilaevis, comparing resistant and susceptible families challenge (CsRC CsSC) control conditions (CsRU CsSU). RNA libraries were constructed using 12 samples isolated from three...
Abstract Turbot ( Scophthalmus maximus ) is a commercially important flatfish species in aquaculture. It has drastic sexual dimorphism, with females growing faster than males. In the present study, we sequenced and de novo assembled female male turbot genomes. The genome was 568 Mb (scaffold N50, 6.2 Mb, BUSCO 97.4%), 584 5.9 96.6%). Using two genetic maps, anchored scaffolds representing 535 onto 22 chromosomes. Annotation of identified 87.8 transposon elements 20,134 genes. We 17,936 gene...
Agrobacterium tumefaciens strain C58 is a Gram-negative soil bacterium capable of inducing tumors (crown galls) on many dicotyledonous plants. The genome A. was re-annotated based the Z-curve method. First, all 'hypothetical genes' were re-identified, and 29 originally annotated recognized to be non-coding open reading frames (ORFs). Theoretical evidence obtained from principal component analysis, clusters orthologous groups proteins occupation, average length distribution showed that these...
Abstract Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits help improve product quality sustainability, we performed a chromosome‐level genome construction for aureovittata . Combining two technologies, PacBio BGISEQ‐500, assembled 649.86 Mb S. sequences with contig N50 22.21 Mb, 98% BUSCO genes were detected total. The initial assembly was then scaffolded into 24 pseudochromosomes using...
Abstract Turbot ( Scophthalmus maximus ), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of intensive breeding scale, turbot exposed to various stresses, which greatly impedes healthy development industry. Here, we present an improved high-quality chromosome-scale genome assembly using a combination PacBio long-read Illumina short-read sequencing technologies. The spans 538.22 Mb comprising 27 contigs with contig N50 size...
Abstract The assembly of W and Y chromosomes poses significant challenges in vertebrate genome sequencing assembly. Here, we successfully assembled the chromosome Verasper variegatus with a length 20.48 Mb by combining population PacBio HiFi data. It was identified as young sex showed signs expansion repetitive sequences. major component Ty3/Gypsy. ancestral Osteichthyes karyotype consists 24 protochromosomes. four Pleuronectiformes species derived from pair homologous protochromosomes...
The mitogen-activated protein kinase (MAPK) gene family performs crucial roles in cell division, migration, development, apoptosis, inflammatory response, and abiotic biotic stress responses. However, very little information is available about the MAPKs turbot ( Scophthalmus maximus ). In this study, 15 Sm MAPKs) were identified throughout whole genome, their basic chemical physical properties subcellular localization illustrated. All contained serine/threonine kinases, catalytic domain...
Chinese tongue sole (Cynoglossus semilaevis) has a ZZ/ZW sex determination system, but the genotypic female (ZW) can be sex-reversed into phenotypic males, namely, pseudomales. Pseudomale fish produce only Z-type sperm not W sperm. However, molecular mechanism is unclear. To screen key genes involved in pseudomale abnormalities, we analysed transcriptomic profiles of and male In comparison to sperm, 592 differentially expressed (DEGs) were identified including 499 upregulated 93...
Long non-coding RNAs (lncRNAs) play crucial roles in a variety of biological processes, including stress response. However, the number, characteristics and stress-related expression lncRNAs turbot are still largely unknown. In this study, total 12,999 were identified at genome-wide level for first time using 24 RNA-seq datasets. Sequence characteristic analyses transcripts showed that lncRNA shorter average length, lower GC content as compared to coding genes. Expression pattern 12 distinct...
Abstract The Japanese flounder is one of the most economically important marine flatfish. However, due to increased frequency extreme weather events and high-density industrial farming, an increasing number environmental stresses have become severe threats healthy development culture industry. Herein, we produced a high-quality chromosome-scale genome using PacBio Circular Consensus Sequencing technologies. assembled spanned 588.22 Mb with contig N50 size 24.35 Mb. In total, 105.89...
As intracellular pathogen recognition receptors (PRRs), nucleotide-binding domain, leucine-rich repeat containing (NLRs, NOD-like receptors) are involved in innate immune responses vertebrates. However, there is no systemic study on NLRs Chinese tongue sole (Cynoglossus semilaevis), a popular maricultured fish China. In the present study, genome-wide survey of was performed C. semilaevis, with identification 29 NLRs, including five genes from NLR-A subfamily (referred to as CsNOD1-5), two...
DATA REPORT article Front. Mar. Sci., 27 October 2022Sec. Marine Biology Volume 9 - 2022 | https://doi.org/10.3389/fmars.2022.1045052