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Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and chromosome evolution

Genomics, Proteomics & Bioinformatics 2023年第3期21卷 470-482页

作者： Ruobing Han Lei Han Xunwu Zhao Qianghui Wang Yanling Xia Heping Li College of Wildlife and Protected Area Northeast Forestry UniversityHarbin 150040China

Despite the scientific and medicinal importance of diploid sika deer(Cervus nippon),its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently *** explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae,we report,for the first time,a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies,which was anchored to 32 homologous groups with a pair of sex chromosomes(XY).Several expanded genes(RET,PPP2R1A,PPP2R1B,YWHAB,YWHAZ,and RPS6)and positively selected genes(eIF4E,Wnt8A,Wnt9B,BMP4,and TP53)were identified,which could contribute to rapid antler growth without carcinogenesis.A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting *** genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer(Cervus elaphus),and the olfactory sensation of sika deer might be more powerful than that of red *** inversion regions containing olfactory receptor genes were also identified,which arose since the *** conclusion,the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler,chromosome evolution,and multi-omics research of cervid animals.

关键词： Allele-specific expression gene Sika deer chromosome evolution Structural variation Rapid antler growth

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Karyotypes of field mice of the genus Apodemus (Mammalia： Rodentia) from China

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Zoological Research 2018年第5期39卷 348-355页

作者： Masaharu Motokawa Yi Wu Masashi Harada Yuta Shintaku Xue-Long Jiang Yu-Chun Li Kyoto University Museum Kyoto University Kyoto 606-8501 Japan Key Laboratory of Conservation and Application in Biodiversity of South China School of Life Sciences Guangzhou University Guangzhou Guangdong 510006 China Laboratory Animal Center Graduate School of Medicine Osaka City University Osaka 545-8585 Japan Wildlife Research Center Kyoto University Sakyo Kyoto 606-8203 Japan Japan Monkey Centre Inuyama Aichi 484-0081 Japan Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China Marine College Shandong University(Weihai) Weihai Shandong 264209 China

Karyotypes of four Chinese species of field mice of the genus Apodemus were examined,including Apodemus chevrieri （diploid chromosome number,2n=48,fundamental number of autosomal arms,FNa=56）,*** （2n=48,FNa=48）,*** （2n=48,FNa=48）,and *** （2n=48,FNa=48）.Karyotypes of ***,***,and *** are reported here for the first time,providing useful information for their species *** the karyotypes of all species of Apodemus in Asia,both in this and previous studies,provides a solid overview of the chromosome evolution and species differentiation of the genus in East *** addition to allopatric speciation,chromosome rearrangements likely played an important role in the formation of the four Apodemus species groups as well as speciation within each group in East *** example,increased centromeric heterochromatin in *** may have contributed to the post-mating reproductive isolation from the *** clade.

关键词： Karyotype chromosome evolution Speciation Taxonomy Field mice

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Thirteen Dipterocarpoideae genomes provide insights into their evolution and borneol biosynthesis

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Plant Communications 2022年第6期3卷 104-119页

作者： Zunzhe Tian Peng Zeng Xiaoyun Lu Tinggan Zhou Yuwei Han Yingmei Peng Yunxue Xiao Botong Zhou Xue Liu Yongting Zhang Yang Yu Qiong Li Hang Zong Feining Zhang Huifeng Jiang Juan He Jing Cai School of Ecology and Environment Northwestern Polytechnical UniversityXi’an 710072China State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoMacaoChina Key Laboratory of Systems Microbial Biotechnology Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308China National Technology Innovation Center of Synthetic Biology Tianjin 300308China Xishuangbanna Tropical Botanical Garden Chinese Academy of SciencesKuming 650223China

Dipterocarpoideae,the largest subfamily of the Dipterocarpaceae,is a dominant component of Southeast Asian rainforests and is widely used as a source of wood,damar resin,medicine,and essential ***,many Dipterocarpoideae species are currently on the IUCN Red List owing to severe degradation of their habitats under global climate change and human *** information regarding these taxa has only recently been reported with the sequencing of four Dipterocarp genomes,providing clues to the function and evolution of these ***,we report on 13 high-quality Dipterocarpoideae genome assemblies,ranging in size from 302.6 to 494.8 Mb and representing the five most species-rich genera in *** dating analyses support the Western Gondwanaland origin of *** on evolutionary analysis,we propose a three-step chromosome evolution scenario to describe the karyotypic evolution from an ancestor with six chromosomes to present-day species with 11 and 7 *** discovered an expansion of genes encoding cellulose synthase(CesA),which is essential for cellulose biosynthesis and secondary cell-wall *** functionally identified five bornyl diphosphate synthase(BPPS)genes,which specifically catalyze the biosynthesis of borneol,a natural medicinal compound extracted from damar resin and oils,thus providing a basis for large-scale production of natural borneol in vitro.

关键词： Dipterocarpoideae genome chromosome evolution cellulose synthase borneol

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High chromosomal evolutionary dynamics in sleeper gobies(Eleotridae)and notes on disruptive biological factors in Gobiiformes karyotypes(Osteichthyes,Teleostei)

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Marine Life Science & Technology 2021年第3期3卷 293-302页

作者： Simião Alefe Soares da Silva Paulo Augusto de Lima-Filho Clóvis Coutinho da Motta-Neto Gideão Wagner Werneck Félix da Costa Marcelo de Bello Cioffi Luiz Antônio Carlos Bertollo Wagner Franco Molina Departamento de Biologia Celular e Genética Centro de BiociênciasUniversidade Federal do Rio Grande do NorteNatalRN59.078-970Brazil Instituto Federal de Ciência e Tecnologia do Rio Grande do Norte Santa CruzRN59200-000Brazil Departamento de Genética e Evolução Universidade Federal de São CarlosRodovia Washington LuísKm 235São CarlosSP13.565-905Brazil

The order Gobiiformes is made up of more than 2200 species,representing one of the most diverse groups among teleost *** biological causes for the tachytelic karyotype evolution of the gobies have not yet been fully *** we expanded cytogenetic data for the Eleotridae family,analyzing the neotropical species Dormitator maculatus,Eleotris pisonis,Erotelis smaragdus,and Guavina *** addition,a meta-analytical approach was followed for elucidating the karyotype diversification versus biological aspects(habitat and egg type)of the *** species *** and *** present 2n=46 acrocentric chromosomes(NF=46),*** 2n=46(36sm+4st+6a;NF=86),and ***,the most divergent karyotype,with 2n=52 acrocentric chromosomes(NF=52).Besides numeric and structural diversification in the karyotypes,the mapping of rDNAs and microsatellites also showed noticeable numerical and positional variation,supporting the high chromosomal evolutionary dynamism of these *** Gobiiformes,karyotype patterns which are more divergent from the basal karyotype(2n=46a)are associated with characteristics less effective to dispersion,such as the benthic *** adaptive characteristics,connected with the organization of the repetitive DNA content in the chromosomes,likely play a synergistic role in the remarkable karyotype diversification of this group.

关键词： chromosome evolution Dispersive potential Goby Karyotype diversification Microsatellites rDNA

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Genome of Triticumurartu and its chromosomal structures and evolution

Genome of Triticumurartu and its chromosomal structures and ...

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2018全国植物生物学大会

作者： Hong-Qing Ling Bin Ma Xiaoli Shi Lingli Dong Hua Sun Hui Liu Zhensheng Li Aimin Zhang Daowen Wang Chengzhi Liang Institute of Genetics and Developmental Biology Chinese Academy of Sciences

Common wheat(Triticumaestivum),one of the most widely cultivated and consumed food crops in the world,is a hexaploid containing A,B and D ***,a wild diploid wheat,is the progenitor of the A subgenome of tetraploid and hexaploid wheat,and plays a central role in wheat evolution,domestication and genetic *** studying the genome evolution and domestication of wheat,we have been working on the genome sequencing of *** since ***,we generated the draft genome of *** the whole-genome shotgun sequencing strategy on the Illumina HiSequation(2000) platform(Ling et al.,2013,Nature 496:87-90).Subsequently,we produced a high-quality genome sequence of *** BAC-by-BAC sequencing strategy combining single molecule real-time sequencing and next-generation mapping technologies(Ling et al.,2018,Nature 557:424-428).The assembled contig sequences were 4.79 Gb with an N50 of 344 kb and scaffold sequences were 4.86 Gb with an N50 of 3.67 *** a high density single nucleotide polymorphism(SNP) genetic map,4.67 Gb(95.9%) of the scaffold sequences were successfully anchored on *** chromosomes,constructing seven chromosome-scale *** comparing collinear segments between *** and its grass relatives,we proposed an evolution model of *** chromosomes,and found that *** and Brachypodium were independently evolved from the grass ancestor with 12 ***,we also found that the ancient genome duplications,which well maintained in rice,sorghum and Brachypodium,were strongly corrupted in *** because of extensive amplifications of transposable elements and widespread gene *** conclusion,we successfully generated a reference genome of the wheat Asubgenome progenitor *** assemblyprovides a valuable resource for studying genome evolution and genetic variation in wheatand related grasses,and promises to facilitate the discovery of genesthat could be useful for wheat improvement.

关键词： Wheat Triticumurartu genome sequencing chromosome evolution

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Remarkable variation of ribosomal（rDNA） DNA in gnetophytes, a distinct lineage of gymnosperms

Remarkable variation of ribosomal（rDNA） DNA in gnetophytes...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Wencai Wang Tao Wan Hannes Becher Alena Kuderova Ilia J.Leitch Sònia Garcia ANDrew R.Leitch Ale? Kova?ík Institute of Clinical Pharmacology Guangzhou University of Chinese Medicine School of Biological and Chemical Sciences Queen Mary University of London Key Laboratory of Southern Subtropical Plant Diversity Fairy Lake Botanical GardenShenzhen & Chinese Academy of Science Sino-Africa Joint Research Center Chinese Academy of Science Institute of Biophysics Academy of Sciences of the Czech Republic Jodrell Laboratory Royal Botanic Gardens

Gnetophytes,comprising genera Ephedra,Gnetum and Welwitschia are an understudied,enigmatic lineage of *** we examined the organization of ribosomal DNA（rDNA） across representative *** applied high throughput sequencing approaches to isolate and reconstruct rDNA units and to determine their intragenomic *** addition,fluorescent in situ hybridization（FISH） and Southern blot hybridization techniques were used to reveal the chromosome and genomic organization of *** found that:（i） the 5 S and 35 S rDNAs were separate in ***,*** and *** and linked in ***;（ii） there was huge variability variability in 5 S rDNA abundance（4,000-100,000 copies per haploid genome） and locus numbers（2-16 sites per diploid genome）;（iii） 5 S rRNA pseudogenes were interspersed between functional genes forming single unit in *** and ***;（iv） in *** internal transcribed spacers（ITS1） of 35 S rDNA were long and intrinsically repetitive while in *** and *** the ITS1 were short without *** conclusion,gnetophytes are distinctive from other gymnosperms and angiosperms as they display a surprisingly high variability in rDNA organization,rDNA copy and locus numbers between genera,with no relationship between copy numbers and genome sizes *** evolution of 5 S rDNA units seems to have led to the amplification of 5 S pseudogenes in both *** and *** patterns of rDNA show both gymnosperm and angiosperm features underlining diversity and distinctness of the group.

关键词： gnetophytes rDNA organization chromosome evolution high through-put sequencing concerted evolution pseudogenes intragenomic diversity

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