ORCID Profile
0000-0003-1643-4631
Current Organisations
Shanghai Jiao Tong University
,
University of Adelaide
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Publisher: Research Square Platform LLC
Date: 20-11-2019
Abstract: Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary ergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.
Publisher: Research Square Platform LLC
Date: 30-08-2019
Abstract: Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary ergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.
Publisher: Research Square Platform LLC
Date: 07-10-2019
Abstract: Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary ergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.
Publisher: Oxford University Press (OUP)
Date: 11-2007
DOI: 10.1534/GENETICS.107.075838
Abstract: As classical phase II detoxification enzymes, glutathione S-transferases (GSTs) have been implicated in insecticide resistance and may have evolved in response to toxins in the niche-defining feeding substrates of Drosophila species. We have annotated the GST genes of the 12 Drosophila species with recently sequenced genomes and analyzed their molecular evolution. Gene copy number variation is attributable mainly to unequal crossing-over events in the large δ and ε clusters. Within these gene clusters there are also GST genes with slowly erging orthologs. This implies that they have their own unique functions or have spatial/temporal expression patterns that impose significant selective constraints. Searches for positively selected sites within the GSTs identified G171K in GSTD1, a protein that has previously been shown to be capable of metabolizing the insecticide DDT. We find that the same radical substitution (G171K) in the substrate-binding domain has occurred at least three times in the Drosophila radiation. Homology-modeling places site 171 distant from the active site but adjacent to an alternative DDT-binding site. We propose that the parallel evolution observed at this site is an adaptive response to an environmental toxin and that sequencing of historical alleles suggests that this toxin was not a synthetic insecticide.
Publisher: Springer Science and Business Media LLC
Date: 29-04-2020
DOI: 10.1038/S41467-020-15848-Y
Abstract: Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.
Publisher: Elsevier BV
Date: 06-2010
DOI: 10.1016/J.JMB.2010.04.020
Abstract: GSTD1 is one of several insect glutathione S-transferases capable of metabolizing the insecticide DDT. Here we use crystallography and NMR to elucidate the binding of DDT and glutathione to GSTD1. The crystal structure of Drosophila melanogaster GSTD1 has been determined to 1.1 A resolution, which reveals that the enzyme adopts the canonical GST fold but with a partially occluded active site caused by the packing of a C-terminal helix against one wall of the binding site for substrates. This helix would need to unwind or be displaced to enable catalysis. When the C-terminal helix is removed from the model of the crystal structure, DDT can be computationally docked into the active site in an orientation favoring catalysis. Two-dimensional (1)H,(15)N heteronuclear single-quantum coherence NMR experiments of GSTD1 indicate that conformational changes occur upon glutathione and DDT binding and the residues that broaden upon DDT binding support the predicted binding site. We also show that the ancestral GSTD1 is likely to have possessed DDT dehydrochlorinase activity because both GSTD1 from D. melanogaster and its sibling species, Drosophila simulans, have this activity.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0CC03566A
Abstract: A cell-inspired microreactor can modulate the phase-oriented transport of reagents at interfaces, affording a powerful tool to optimize reaction selectivity.
Publisher: Springer Science and Business Media LLC
Date: 11-2007
DOI: 10.1038/NATURE06341
No related grants have been discovered for Li Xin-Hao.