A5086749592- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Plant Reproductive Biology
- Parasite Biology and Host Interactions
- Wheat and Barley Genetics and Pathology
- Lipid metabolism and biosynthesis
- Plant Molecular Biology Research
- Plant Pathogenic Bacteria Studies
- Photosynthetic Processes and Mechanisms
- Parallel Computing and Optimization Techniques
- Anaerobic Digestion and Biogas Production
- Peroxisome Proliferator-Activated Receptors
- Plant Virus Research Studies
- Plant Disease Resistance and Genetics
- Genetic diversity and population structure
- Fault Detection and Control Systems
- Forensic and Genetic Research
- MicroRNA in disease regulation
- Plant nutrient uptake and metabolism
- Aquatic Invertebrate Ecology and Behavior
- Plant Gene Expression Analysis
- Advanced Control Systems Optimization
Bioscience (China)
2019-2024
Nextomics Biosciences (China)
2020-2024
Grandomics (China)
2019-2024
Zhongkai University of Agriculture and Engineering
2023
Chinese Academy of Fishery Sciences
2020
Institute of Hydrobiology
2018-2019
Chinese Academy of Sciences
2018-2019
Wuhan Polytechnic University
2016-2017
Southeast University
2006
Although long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently corrects sequence errors in assembled reads. This new consists of two interlinked modules are designed to score and count K-mers quality short reads, polish genome assemblies containing large numbers base errors.When evaluated for the speed efficiency using human plant (Arabidopsis thaliana) genomes, NextPolish...
Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting 251-accession panel comprising both cultivated wild species Asian African rice. Our reveals extensive structural variations (SVs) gene presence/absence variations. Additionally, our enables the accurate identification nucleotide-binding leucine-rich repeat genes characterization their inter-...
Long-read sequencing data, particularly those derived from the Oxford Nanopore platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient correction and assembly tool for noisy long reads, which achieves a level of accuracy in genome assembly. We apply NextDenovo assemble 35 diverse human genomes around world using long-read data. These allow us identify landscape segmental duplication gene copy number variation modern populations. The use should pave way population-scale
Abstract Long read sequencing data, particularly those derived from the Oxford Nanopore (ONT) platform, tend to exhibit a high error rate. Here, we present NextDenovo, highly efficient correction and assembly tool for noisy long reads, which achieves level of accuracy in genome assembly. NextDenovo can rapidly correct reads; these corrected reads contain fewer errors than other comparable tools are characterized by chimeric alignments. We applied quality reference genomes 35 diverse humans...
Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes many crops have been generated, such work in has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing Hi-C technologies, we generated reference-quality genome assembly hulless common oat, comprising 21 pseudomolecules with total length 10.76 Gb contig N50 75.27 Mb. We also produced...
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution human genetic architecture and diversity. We present such study 50 species spanning 38 genera 14 families, including 27 first reported here, with many from previously less well represented groups, New World monkeys Strepsirrhini. Our analyses reveal heterogeneous rates genomic rearrangement gene across lineages. Thousands genes under positive selection in different lineages play...
Abstract Background The availability of reference genomes has revolutionized the study biology. Multiple competing technologies have been developed to improve quality and robustness genome assemblies during past decade. 2 widely used long-read sequencing providers—Pacific Biosciences (PacBio) Oxford Nanopore Technologies (ONT)—have recently updated their platforms: PacBio enables high-throughput HiFi reads with base-level resolution >99%, ONT generated as long Mb. We applied...
Diosgenin saponins isolated from Dioscorea species such as D. zingiberensis exhibit a broad spectrum of pharmacological activities. Diosgenin, the aglycone diosgenin saponins, is an important starting material for production steroidal drugs. However, how plants produce and origin evolution saponin biosynthetic pathway remain mystery. Here we report high-quality, 629-Mb genome anchored on 10 chromosomes with 30 322 protein-coding genes. We reveal that synthesized in leaves ('source'), then...
Abstract Elephant grass (2 n = 4 x 28; Cenchrus purpureus Schumach.), also known as Napier grass, is an important forage and potential energy crop in tropical subtropical regions of Asia, Africa America. However, no study has yet reported a genome assembly for elephant at the chromosome scale. Here, we report high‐quality chromosome‐scale with total size 1.97 Gb 1.5% heterozygosity rate, obtained using short‐read sequencing, single‐molecule long‐read sequencing Hi‐C conformation capture....
Geese evolved from migratory birds, and when they consume excessive high-energy feed, glucose is converted into triglycerides. A large amount of triglyceride deposition can induce incomplete oxidation fatty acids, leading to lipid accumulation in the liver subsequent formation liver. In Chaoshan region Guangdong, China, Shitou geese develop a unique form through 24 h overfeeding brown rice. To investigate mechanisms underlying geese, we collected samples normally fed overfed geese. The...
A plant can be thought of as a colony comprising numerous growth buds, each developing to its own rhythm. Such lack synchrony impedes efforts describe core principles morphogenesis, dissect the underlying mechanisms, and identify regulators. Here, we use minimalist known angiosperm overcome this challenge provide model system for morphogenesis. We present detailed morphological description monocot Wolffia australiana, well high-quality genome information. Further, developed plant-on-chip...
Eucommia ulmoides Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report high-quality chromosome-level female genome of E. obtained by PacBio Hi-C technologies. The size the assembly was 1.01 Gb with 17 pseudochromosomes 31,665 protein coding genes. In addition, technology used reassemble male released in 2018. reassembled 1.24 superscaffold N50 (48.30 Mb), which increased 25.69 times, number predicted genes 11,266. Genome evolution...
Abstract The morphology of Nyctotheroides hubeiensis (Acta Hydrobiol. Sin. 1998, 22(suppl.):187), collected from the rectum Phelophylax nigromaculatus , is presented in this paper based on detailed morphological information and molecular data. Our phylogenetic analysis showed that N. fell into clade, which was strongly supported as monophyletic clustered basal to genera Nyctotherus Clevelandella . Also, monophyly Order Clevelandellida affinity parasitic nyctotherids free‐living metopids were...
Abstract The availability of reference genomes has revolutionized the study biology. Multiple competing technologies have been developed to improve quality and robustness genome assemblies during last decade. two widely-used long read sequencing providers – Pacbio (PB) Oxford Nanopore Technologies (ONT) recently updated their platforms: PB enable high throughput HiFi reads with base-level resolution >99% ONT generated as 2 Mb. We applied up-to-date platforms one single rice individual,...
Abstract Background Oat ( Avena sativa , 2 n =6 x =42) is an important crop, and with its wild relatives including A. longiglumis (ALO, =14), has advantageous agronomic nutritional traits. A de-novo chromosome-level ALO genome assembly was made to investigate diversity structural variation between species other Poaceae in evolutionary context, develop genomic resources identify the pangenome economic traits within Pooideae. Results The 3.85 gigabase (seven pseudo-chromosomes), contained...
In this paper, we present transcriptome data for Balantidium ctenopharyngodoni Chen, 1955 collected from the hindgut of grass carp (Ctenopharyngodon idella). We evaluated sequence quality and de novo assembled a preliminary transcriptome, including 43.3 megabits 119,141 transcripts. Then obtained final 17.7 35,560 transcripts, by removing contaminative redundant sequences. Phylogenomic analysis based on supermatrix with 132 genes comprising 53,873 amino acid residues phylogenetic SSU rDNA 27...
Abstract Background Blowflies (Diptera: Calliphoridae) are the most commonly found entomological evidence in forensic investigations. Distinguished from other blowflies, Aldrichina grahami has some unique biological characteristics and is a species of importance. Its development rate, pattern, life cycle can provide valuable information for estimation minimum postmortem interval. Findings Herein we chromosome-level genome assembly A. that was generated by Pacific BioSciences sequencing...
In this study, we present a de novo genome assembly of Gymnocypris przewalski using long‐read PacBio sequencing technology with Genome-wide high throughput chromosome conformation capture correction. The resulted in sequence contiguity and accuracy 23 chromosomes size 945 Mb. This work is the first chromosome‐level study Schizothoracine fishes from Qinghai-tibet plateau (QTP). Phylogenetic analysis showed that species differentiation events between G. przewalskii Cyprinus carpio occurred at...
Abstract A plant can be thought of as a colony comprising numerous growth buds, each developing to its own rhythm. Such lack synchrony impedes efforts describe core principles morphogenesis, dissect the underlying mechanisms, and identify regulators. Here, we use tiniest known angiosperm overcome this challenge provide an ideal model system for morphogenesis. We present detailed morphological description monocot Wolffia australiana , well high-quality genome information. Further, developed...