A5100352324- Genomics and Phylogenetic Studies
- Aquaculture disease management and microbiota
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- CRISPR and Genetic Engineering
- Genetic and phenotypic traits in livestock
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Cancer-related molecular mechanisms research
- Plant Molecular Biology Research
- Legume Nitrogen Fixing Symbiosis
- Plant Disease Resistance and Genetics
- interferon and immune responses
- RNA and protein synthesis mechanisms
- Plant Gene Expression Analysis
- Photosynthetic Processes and Mechanisms
- Plant biochemistry and biosynthesis
- Plant-Microbe Interactions and Immunity
- Cancer Research and Treatments
- Wheat and Barley Genetics and Pathology
- Metabolomics and Mass Spectrometry Studies
- Plant Pathogens and Fungal Diseases
- Plant and Fungal Species Descriptions
- Pluripotent Stem Cells Research
Qingdao Agricultural University
2012-2025
National Clinical Research Center for Digestive Diseases
2025
Chinese Academy of Medical Sciences & Peking Union Medical College
2013-2025
Nanjing Forestry University
2016-2025
Yangzhou University
2022-2025
Chinese Academy of Sciences
2015-2025
Shandong First Medical University
2019-2025
BGI Group (China)
2016-2025
Yancheng Teachers University
2024-2025
University of Chinese Academy of Sciences
2014-2025
This paper reports the genome sequence of domesticated tomato, a major crop plant, and draft for its closest wild relative; comparative genomics reveal very little divergence between two genomes but some important differences with potato genome, another food in genus Solanum. Tomato (Solanum lycopersicum) is plant model system fruit development. Solanum one largest angiosperm genera1 includes annual perennial plants from diverse habitats. Here we present high-quality relative,...
The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of microbiome in relation diseases have not systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals with atherosclerotic disease (ACVD) 187 healthy controls. ACVD deviates status by increased abundance Enterobacteriaceae Streptococcus spp. and, functionally, potential for metabolism or transport several molecules important...
Two draft sequences of Gossypium hirsutum, the most widely cultivated cotton species, provide insights into genome structure, rearrangement, gene evolution and fiber biology. hirsutum has proven difficult to sequence owing its complex allotetraploid (AtDt) genome. Here we produce a using 181-fold paired-end assisted by fivefold BAC-to-BAC high-resolution genetic map. In our assembly 88.5% 2,173-Mb scaffolds, which cover 89.6%∼96.7% AtDt genome, are anchored oriented 26 pseudochromosomes....
David Bertioli and colleagues report the genomes of Arachis duranensis ipaensis, diploid ancestors cultivated peanut, hypogaea. Their analyses are a first step in understanding evolution peanut's tetraploid genome. Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes total size ∼2.7 Gb. This makes assembly chromosomal pseudomolecules very challenging. As foundation to genome we sequences its ipaensis). We show that these similar A B use them identify...
Mapping the mammalian brain The diverse physiology of is reflected in its complex organization at regional, cellular, and subcellular levels. Sjöstedt et al. combined data—both newly acquired from other large-scale mapping projects—from transcriptomics, single-cell genomics, situ hybridization, antibody-based protein profiling to map molecular profiles human, pig, mouse brain. analysis consistent with a conserved basic architecture during evolution, but it does show differences regional gene...
Chinese hamster ovary (CHO)-derived cell lines are the preferred host cells for production of therapeutic proteins. Here we present a draft genomic sequence CHO-K1 ancestral line. The assembly comprises 2.45 Gb sequence, with 24,383 predicted genes. We associate most assembled scaffolds 21 chromosomes isolated by microfluidics to identify chromosomal locations Furthermore, investigate genes involved in glycosylation, which affect protein quality, and viral susceptibility genes, relevant...
The genome sequence and its analysis of the diploid wild wheat Triticum urartu (progenitor A genome) represent a tool for studying complex, polyploid genomes should be valuable resource genetic improvement wheat. hexaploid bread aestivum, designated AABBDD, evolved as result hybridization between three ancestral grasses. Two papers published in issue Nature present sequences two these progenitors. First, T. (ancestor genome), which resembles cultivated more strongly than either Aegilops...
Completion of genome sequences for the diploid Setaria italica reveals features C4 photosynthesis that could enable improvement polyploid biofuel crop switchgrass (Panicum virgatum). The genetic basis biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted. Foxtail millet (Setaria italica), a member Poaceae grass family, an important food fodder in arid regions has potential use as biofuel. It model system other...
An instrument for whole-genome optical mapping is used to assemble the genome of domestic goat into super-long scaffolds. We report ∼2.66-Gb sequence a female Yunnan black goat. The was obtained by combining short-read sequencing data and from high-throughput instrument. facilitated assembly super-scaffolds >5× longer N50 metric than scaffolds augmented fosmid end (scaffold = 3.06 Mb, super-scaffold 16.3 Mb). Super-scaffolds are anchored on chromosomes based conserved synteny with cattle,...
Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form wool represent distinct class animals that have specialized digestive organ, rumen, carries out initial digestion plant material. We developed analyzed high-quality reference sheep genome transcriptomes from 40 different tissues. identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. also involved lipid metabolism had been amplified and/or altered tissue expression...
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India South Asia. We report the ∼1.79 Gb draft whole genome sequence reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. highlight substantial enrichment wax biosynthesis genes, may contribute to heat drought tolerance this crop. resequenced analyzed 994 pearl lines, enabling insights into population structure,...
Zhong-Jian Liu, Lai-Qiang Huang, Yi-Bo Luo, Hong-Hwa Chen and Yves Van de Peer report the first genome sequence of a crassulacean acid metabolism (CAM) plant, orchid Phalaenopsis equestris. They identify genes encoding CAM pathway enzymes find that gene duplication was likely key process in evolution photosynthesis. Orchidaceae, renowned for its spectacular flowers other reproductive ecological adaptations, is one most diverse plant families. Here we present tropical epiphytic equestris,...
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they generally colossal. Here, we report on of Azolla filiculoides and Salvinia cucullata (Salviniales) present evidence for episodic whole-genome duplication in ferns-one at base 'core leptosporangiates' one specific Azolla. One fern-specific gene identified, recently shown confer high insect resistance, seems have been derived from bacteria through horizontal transfer. coexists a...
Dinoflagellates are important components of marine ecosystems and essential coral symbionts, yet little is known about their genomes. We report here on the analysis a high-quality assembly from 1180-megabase genome Symbiodinium kawagutii. annotated protein-coding genes identified Symbiodinium-specific gene families. No whole-genome duplication was observed, but instead we found active (retro)transposition family expansion, especially in processes for successful symbiosis with corals. also...
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome thought to play an important role in promoting citrus growth and health. Here, we report comprehensive analysis of the structural functional composition microbiome. We use both amplicon deep shotgun metagenomic sequencing bulk soil samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria Bacteroidetes. The core...
Leif Andersson and colleagues report the genome sequence of ruff, a bird species with three male morphs different reproductive strategies. Satellite faeder differ from common independent morph by 4.5-Mb inversion that occurred approximately 3.8 million years ago, multiple genetic changes within this inverted region are associated satellite morphs. The ruff is Palearctic wader spectacular lekking behavior where highly ornamented males compete for females1,2,3,4. This has one most remarkable...