A5055680598- Chromosomal and Genetic Variations
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Wheat and Barley Genetics and Pathology
- Animal Genetics and Reproduction
- Genetics and Plant Breeding
- Animal Behavior and Reproduction
- Genomics and Chromatin Dynamics
- Genetic and phenotypic traits in livestock
- Advanced biosensing and bioanalysis techniques
- Plant and animal studies
- Livestock and Poultry Management
- CRISPR and Genetic Engineering
- Congenital heart defects research
- Paleontology and Evolutionary Biology
- Single-cell and spatial transcriptomics
- Sperm and Testicular Function
- Genetic and Environmental Crop Studies
- Agronomic Practices and Intercropping Systems
- Species Distribution and Climate Change
- Insect behavior and control techniques
- Developmental Biology and Gene Regulation
- Agroforestry and silvopastoral systems
Southwest University
2022-2024
University of Vienna
2018-2023
Hebei University of Engineering
2022
Fujian Normal University
2022
Zhejiang University
2018-2021
Kunming Institute of Zoology
2017
Chinese Academy of Sciences
2017
China National GeneBank
2014-2015
Uppsala University
2015
Wuhan University
2014
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The genome is principally characterized by its constrained size, which predominantly arose because lineage-specific erosion repetitive elements, large segmental deletions, gene loss. Avian furthermore show a remarkably high degree evolutionary stasis at levels...
Significance Old World (sub)tropical fungus-growing termites owe their massive ecological footprints to an advanced symbiosis with Termitomyces fungi. They also have abundant gut bacteria, but the complementarity roles of these symbionts remained unclear. We analyzed genomic potential for biomass decomposition in a farming termite, its fungal symbiont, and bacterial communities. found that plant conversion is mostly multistage complementary cooperation between termite farmers primarily...
Bread wheat is one of the most important and broadly studied crops. However, due to complexity its genome incomplete collection wild populations, bread landscape domestication history remain elusive.By investigating whole-genome resequencing data 93 accessions from worldwide populations diploid tetraploid progenitors, together with 90 published exome-capture data, we find that B subgenome has more variations than A D subgenomes, including SNPs deletions. Population genetics analyses support...
Microchromosomes are prevalent in nonmammalian vertebrates [P. D. Waters et al. , Proc. Natl. Acad. Sci. U.S.A. 118 (2021)], but a few of them missing bird genome assemblies. Here, we present new chicken reference containing all autosomes, Z and W chromosome, with gaps closed except for the W. We identified ten small microchromosomes (termed dot chromosomes) distinct sequence epigenetic features, among which six were newly assembled. Those chromosomes exhibit extremely high GC content level...
Abstract Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs increasing efficiency of sequencing technologies now enable assembling genomes unprecedented quality contiguity. However, the difficulty in repeat‐rich GC‐rich regions (genomic “dark matter”) limits insights into evolution genome structure regulatory networks. Here, we compare available (short/linked/long reads proximity ligation maps) combinations thereof...
Abstract Background The origin of sex chromosomes requires the establishment recombination suppression between proto-sex chromosomes. In many fish species, chromosome pair is homomorphic with a recent origin, providing species for studying how and why evolved in initial stages differentiation, but this accurate sequence assembly X Y (or Z W) chromosomes, which may be difficult if they are recently diverged. Results Here we produce haplotype-resolved genome zig-zag eel ( Mastacembelus armatus...
The karyotype of most birds has remained considerably stable during more than 100 million years' evolution, except for some groups, such as parrots. evolutionary processes and underlying genetic mechanism chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies four parrot genomes, we uncover frequent chromosome fusions fissions, with them occurring independently among lineages. increased activities parrots likely associated...
The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve nearly complete chromosomal genomes three species, one which best recapitulates 17 chordate ancestor linkage groups. We reconstruct fusions, retention, or rearrangements between descendants whole-genome duplications, gave rise to extant microchromosomes likely existed ancestor. Similar vertebrates, genome gradually establishes its...
BackgroundPenguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an life, some have successfully adapted hostile environments Antarctica. To study phylogenetic population history molecular basis their adaptations Antarctica, we sequenced genomes two Antarctic dwelling penguin species, Adélie [Pygoscelis adeliae] emperor [Aptenodytes forsteri].
Abstract Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One these magnificent examples transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with feathers. By analysing 48 bird genomes, we identified millions avian-specific highly conserved elements (ASHCEs) predominantly (>99%) reside in non-coding regions. Many ASHCEs show...
Abstract Tilapias are one of the most farmed fishes that coined as “aquatic chicken” by food industry. Nile tilapia and blue exhibit very recent transition sex chromosome systems since their divergence approximately five million years ago, making them a great model for elucidating molecular evolutionary mechanisms turnovers. Studies sex‐determining pathways also critical developing genetic control in aquaculture. We report here newly produced genomes integrate long‐read sequencing chromatin...
Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration heterogametic chromosome, as is seen for Y in mammals and W most birds. Unlike other birds, paleognaths (ratites tinamous) possess large nondegenerate regions on their chromosomes (PARs or pseudoautosomal regions). It remains unclear why these PARs are retained over >100 Myr, how this retention impacts within system. To address puzzle, we analyzed Z gene expression across 12...
Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but pair much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution chromosome architectures between ducks chickens, birds mammals, we produced nearly complete chromosomal assembly female Pekin duck by combining long-read sequencing multiplatform scaffolding techniques.
Emu and other ratites are more informative than any birds in reconstructing the evolution of ancestral avian or vertebrate karyotype because their much slower rate genome evolution. Here, we generated a new chromosome-level assembly female emu, estimated tempo chromosome across major phylogenetic branches, by comparing it to assemblies 11 bird one turtle species. We found exhibited lowest numbers intra- inter-chromosomal changes among since divergence with turtles. The small-sized gene-rich...
There is increasing evidence that dosage compensation not a ubiquitous feature following sex chromosome evolution, especially in organisms where females are the heterogametic sex, like birds. Even when it occurs, can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may reflect expression at protein level. Here, we used liquid chromatography-tandem mass spectrometry detect quantify expressed...
Lignification of cellulose limits the effective utilisation fibre in plant cell wall. Lignocellulose-degrading bacteria secrete enzymes that decompose lignin and have potential to improve digestibility. Therefore, this study aimed investigate effect whole-plant corn silage inoculated with lignocellulose-degrading on growth performance, rumen fermentation, microbiome sheep. Twelve 2-month-old male hybrid sheep (Dorper ♂ × small-tailed Han ♀) were randomly assigned into two dietary groups (n =...
Abstract Background The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies chickens. These have provided insight into etiology traits commercial importance. However, use single genome does not capture diversity present among modern breeds, many which accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited cataloging simple variants such single-nucleotide short insertions...
Abstract Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology behavior of bird species. Core waterbirds, major clade birds, share common characteristics being sexually monomorphic having lower levels inter-sexual conflict, yet their chromosome evolution remains poorly understood. Here, by we analyse chromosome-level assembly female crested ibis (Nipponia nippon), typical core waterbird. We identify neo-sex resulting from fusion microchromosomes with...
Stereo-seq is the state-of-the-art technique, which allows capturing of spatial transcriptomic data at sub-cellular resolution and in large scale view. FFPE technique recently launched with capability to obtain spatially resolved gene expression tissue sections. However, omic information limited transcriptome. To delineate molecular hierarchy from transcriptome phenome, we present protocol that implements nine-plex immunofluorescence staining detection transcriptomics one section (short for...
Sex chromosomes are unique genomic regions with sex-specific or sex-biased inherent patterns and expected to be more frequently subject selection. Substantial knowledge on the evolutionary of sex-linked genes have been gained from studies male heterogametic systems (XY male, XX female), but understanding role selection in evolution female-heterogametic sex (ZW female, ZZ male) is limited. Here we collect W-linked 27 birds, covering three major avian clades: Neoaves (songbirds), Galloanserae...
Chromosome size and morphology vary within among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in tribe Oreochromini share an unusual giant chromosome that ∼3 times longer than other chromosomes. This functions as a sex some species. We test two hypotheses how this may have evolved. The first hypothesis proposes it evolved by accumulating repetitive elements recombination was reduced around dominant determination locus,...
Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow rate chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The common ancestor had proto-vertebrate-like karyotype, including presence 18 microchromosome pairs. X chromosome conversed shared by all suggesting likely origin sex at...