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中国畜牧兽医学会兽医寄生虫学分会第十三次学术研讨会

作者： Wang Huibao Song Junke Lin Qing Yu Sanke Zhao Guanghui College of Veterinary Medicine Northwest A&F University

Pseudanoplocephala crawfordi,a common parasite of free-range pigs and wild boar inhabiting in small intestines,can causes weight loss,growth obstructed,abdominal pain,diarrhea and even death(Jiang et al.,1990;Wang,2002).More importantly,*** is an important zoonotic parasite,with 21 human cases identified in Liaoning,Henan,and Shaanxi provinces of China successively,posing significant public health *** identification of parasites is central for prevention and control of parasitic *** DNA(mtDNA) are robust genetic markers in investigating phylogenetic relationships at different taxonomic levels,especially when concatenated protein-coding sequences are used for phylogenetic analysis(Liu GH et al.,2011;Zhao GH et al.,2012;Zhao GH et al.,2014).In the present study,based on Long-range PCR-coupled sequencing and bioinformatic methods,we characterized the complete mitochondrial(mt) genome of *** from *** complete mt genome of *** was 14,192 bp in *** mt genomes were circular and encodes 36 genes,including 12 protein-coding genes(cox1-3,nad1-6,nad4 L,atp6 and cytb),22 transfer RNA genes(two leucine- and serine-specifying tRNAs)and two ribosomal RNA *** genes were distributed in the coding strand with same transcription direction,typical for other tapeworms reported to *** nucleotide compositions of the complete mt DNA sequences are biased toward T and A,with T being the most favored nucleotide and C as the least *** analysis of the concatenated amino acid sequences using the Bayesian inference(BI) method showed that *** was closely related to the family *** that the taxonomic status of *** has been controversial only based on morphological features,the mt genome obtained here not only will provide novel molecular markers to accurately ascertain the phylogenetic position of this parasite,but also have the potential to speed up the development

关键词： Pseudanoplocephala crawfordi mitochondrial genome Phylogenetic analyses

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mitochondrial genomes of Tapes dorsatus and Cardita variegata:insights into Heteroconchia phylogeny

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Journal of Oceanology and Limnology 2024年第3期42卷 943-959页

作者： Xumin WANG Hua ZHANG Xindong TENG Wenhui SUN Zhikai XING Shuang WANG Xiumei LIU Jiangyong QU Lijun WANG College of Life Science Yantai UniversityYantai 264005China Qingdao International Travel Healthcare Center Qingdao 266071China

Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve *** relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between *** the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput *** is the first mitochondrial genome belonging to the family Carditidae to be *** used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of *** results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,*** analysis show that gene arrangement within Venerida was highly ***-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 *** results provide evidence of the internal relationships of Heteroconchia.

关键词： Tapes dorsatus Cardita variegata mitochondrial genome phylogeny

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Phylogenomic resolution of Imparidentia(Mollusca:Bivalvia)diversifcation through mitochondrial genomes

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Marine Life Science & Technology 2023年第3期5卷 326-336页

作者： Yu Wang Yi Yang Lingfeng Kong Takenori Sasaki Qi Li Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China Laboratory for Marine Fisheries Science and Food Production Processes Laoshan LaboratoryQingdao 266237China The University Museum The University of TokyoTokyo 113-0033Japan

Despite signifcant advances in the phylogenomics of bivalves over the past decade,the higher-level phylogeny of Imparidentia(a superorder of Heterodonta)remains ***,a total of fve new mitochondrial sequences(Chama asperella,Chama limbula,Chama dunkeri,Barnea manilensis and Ctena divergens)was added to provide resolution in nodes that required additional *** the monophyly of Lucinida remains less clear,the results revealed the overall backbone of the Imparidentia tree and the monophyly of ***,most relationships among the fve major Imparidentia lineages—Lucinida,Cardiida,Adapedonta,Myida and Venerida—were addressed with a well-supported *** relationships of Imparidentia recovered Lucinidae as the sister group to all remaining imparidentian *** is a sister group to other imparidentian bivalves(except Lucinidae species)which is split into Cardiida,Adapedonta and the divergent clade of *** was comprised of Venerida and Myida,the former of which now also contains Chamidae as the sister group to all the remaining venerid ***,molecular divergence times were inferred by calibrating nine nodes in the Imparidentia tree of life by extinct *** origin of these major clades ranged from Ordovician to Permian with the diversifcation through the Palaeozoic to ***,the results obtained in this study demonstrate a better-resolved Imparidentia phylogeny based on mitochondrial genomes.

关键词： Imparidentia Phylogeny mitochondrial genome

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Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals(Octocorallia:Alcyonacea):Insights into slow evolution and adaptation to extreme deep-sea environments

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Zoological Research 2024年第1期45卷 215-225页

作者： Zhan-Fei Wei Kai-Wen Ta Nan-Nan Zhang Shan-Shan Liu Liang Meng Kai-Qiang Liu Chong-Yang Cai Xiao-Tong Peng Chang-Wei Shao National Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China BGI-Qingdao BGI-ShenzhenQingdaoShandong 266555China Institute of Deep-Sea Science and Engineering Chinese Academy of SciencesSanyaHainan 572000China

A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea(SCS).Based on mitochondrial genomic characteristics,morphological examination,and sclerite scanning electron microscopy,the samples were categorized into four suborders(Calcaxonia,Holaxonia,Scleraxonia,and Stolonifera),and identified as 9 possible new cold-water coral *** of GC-skew dissimilarity,phylogenetic distance,and average nucleotide identity(ANI)revealed a slow evolutionary rate for the octocoral mitochondrial *** nonsynonymous(Ka)to synonymous(Ks)substitution ratio(Ka/Ks)suggested that the 14 protein-coding genes(PCGs)were under purifying selection,likely due to specific deep-sea environmental *** analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b(cyt b)and DNA mismatch repair protein(mutS)may be influenced by environmental factors in the context of deep-sea species *** study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.

关键词： mitochondrial genome Alcyonacea Ka/Ks evolution Environmental factors

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Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution

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The Crop Journal 2023年第6期11卷 1782-1792页

作者： Yanlei Feng Yukang Wang Hejun Lu Jun Li Delara Akhter Fang Liu Ting Zhao Xingxing Shen Xiaobo Li James Whelan Tianzhen Zhang Jianping Hu Ronghui Pan College of Agriculture and Biotechnology&ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 310058/311215ZhejiangChina Zhejiang Laboratory Hangzhou 311121ZhejiangChina Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024ZhejiangChina Department of Genetics and Plant Breeding Sylhet Agricultural UniversitySylhet 3100Bangladesh State Key Laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 450000HenanChina Institute of Biology Westlake Institute for Advanced StudyHangzhou 310024ZhejiangChina College of Life Science Zhejiang UniversityHangzhou 310058ZhejiangChina Michigan State University Department of Energy Plant Research Laboratory and Plant Biology DepartmentEast LansingMI 48824USA

Cotton is a major crop that provides the most important renewable textile fibers in the *** of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin,evolution,and cultivation of polyploid *** studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber ***,with only a few mitogenomes assembled in the cotton genus Gossypium,our knowledge about their roles in cotton evolution and speciation is still *** close this gap,here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades(A–G,K,and AD genomes)and 5 cotton relatives using short and long sequencing *** analyses uncovered a high level of mitochondrial gene sequence conservation,abundant sequence repeats and many insertions of foreign sequences,as well as extensive structural variations in cotton *** sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general,while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content,RNA editing,and gene expression ***,we further revealed the specific presence and expression of two novel mitochondrial open reading frames(ORFs)in lint-fiber cotton ***,these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.

关键词： Cotton evolution Cotton phylogeny Lint fiber cotton mitochondrial genome mitochondrial genes

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Novel evolutionary insights into nemacheilid cavefi sh: evidence from comparative analysis of mitochondrial genomes

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Journal of Oceanology and Limnology 2022年第4期40卷 1640-1653页

作者： Lei ZHOU Shihui HUANG Qing WANG Zhenhai LI Zongyang LI Anyou HE Jiehu CHEN Li LIU Keshu ZOU Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation College of Marine SciencesSouth China Agricultural UniversityGuangzhou 510642China Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture Guangxi Academy of Fishery SciencesNanning 530021China Science Corporation of Gene Guangzhou 510000China

Cavefi sh can be important models for understanding the relationships among evolution,adaptation,and development in extreme ***,cavefi sh remain poorly studied,particularly at the genome ***,we sequenced the complete mitogenome of three cavefi sh in the family Nemacheilidae(Paranemachilus pingguoensis,Oreonectes polystigmus,and Heminoemacheilus longibarbatus),which were collected from karst caves in South *** mitogenomes each contained 37 genes(13 protein coding,22 tRNA,and two rRNA genes)and a single control region,with the same genetic arrangement and distribution as those found in *** non-synonymous/synonymous mutation ratios(Ka/Ks)of the mitogenomes indicated that the protein-coding genes(PCGs)of the three cavefi sh evolved under purifying *** mitogenomes of the three cavefi sh exhibit nucleotide composition biases for PCGs,tRNAs,rRNAs,and the whole genome,indicating that the mitochondrial DNA might have been subjected to evolutionary selection in response to extreme cave *** time and evolutionary history analyses suggested that the speciation and diversifi cation of the cavefi sh coincided with the Miocene uplift of the southern Qinghai-Tibet Plateau,which greatly changed cave ***,our study sheds light on the mitogenomes,phylogeny,and evolutionary history of nemacheilid cavefi sh.

关键词： cavefish mitochondrial genome evolution Nemacheilidae

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Evolutionary timescale of chalcidoid wasps inferred from over one hundred mitochondrial genomes

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Zoological Research 2023年第3期44卷 467-482页

作者： Jia-Chen Zhu Hui Xiao Pu Tang Xiao-Fei Li Xuan-Kun Li Chao-Dong Zhu Qiong Wu Jin-Hua Xiao Cornelis van Achterberg Da-Wei Huang Xue-Xin Chen State Key Laboratory of Rice Biology Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insect PestsProvincial Key Lab of Biology of Crop Pathogens and Insect Pests of ZhejiangInstitute of Insect SciencesZhejiang UniversityHangzhouZhejiang 310058China Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101China Florida Museum of Natural History University of FloridaGainesvilleFL 32611 USA College of Life Sciences Nankai UniversityTianjin 300071China

Chalcidoidea is one of the most biologically diverse groups among *** are characterized by extraordinary parasitic lifestyles and extensive host ranges,among which several species attack plants or serve as ***,higher-level chalcidoid relationships remain ***,we performed mitochondrial phylogenomic analyses for major clades(18out of 25 families)of Chalcidoidea based on 139 mitochondrial *** compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree *** phylogenetic results supported the monophyly of 16families and polyphyly of Aphelinidae and *** preferred topology recovered the relationship(Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+remaining Chalcidoidea))).The monophyly of Agaonidae and Sycophaginae was rejected,while the gall-associated((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae))relationship was supported in most results.A six-gene inversion may be a synapomorphy for most families,whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper *** estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of *** hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of *** state reconstruction analyses supported the hypothesis that gallinducers were mainly derived from parasitoids of gallinducers,while other gall-inducers were derived from phytophagous *** together,these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.

关键词： mitochondrial genome Chalcidoidea Compositional heterogeneity Divergence time Evolution of host and gall associations

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Assembly and marker analysis of mitochondrial genomes provide insights into origin,evolution and spread of Brassica juncea(L.)*** Coss.

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The Crop Journal 2022年第3期10卷 611-616页

作者： Liang You Liu Yang Fangying Liu Lei Kang Hao Chen Bin Yang Qian Yang Zhongsong Liu College of Agronomy Hunan Agricultural UniversityChangsha 410128HunanChina Guizhou Institute of Oil Crops Guizhou Academy of Agricultural SciencesGuiyang 550000GuizhouChina

The release of mitochondrial genome sequences provides the basis for characterizing interspecific and intraspecific variation in Brassica mitochondrial ***,few ***(mustard)mitochondrial genomes have been *** assembled the mitochondrial genomes of three *** subspecies and compared them with previously published *** genomes were phylogenetically classified into A,B,C,and Bna *** variant sites,a transversion(C→A)at nt 79,573 and a 31-bp copy-number variation between nts 65,564 and 65,596,were *** on these variant sites,mitotype-specific sequence markers were developed to characterize the variation among worldwide 558 *** *** mitochondrial genome types(mitotypes MT1–MT3)were *** terms of geographical distribution,MT1 and MT2 accessions were distributed mainly to the north and MT3 to the south of 34°*** mustards carried only MT1,leaf and stem mustards carried mainly MT3,and seed mustards carried all three mitotypes,implying that the mitotypes underwent selection during *** domestication.A new form of oil mustard evolved by hybridization between two gene pools in southwest China.

关键词： Brassica juncea mitochondrial genome Mitotypes Molecular markers Migration routes

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Relaxation of Selective Constraint on the Ultra-Large mitochondrial genomes of Arcidae (Mollusca: Bivalvia)

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Journal of Ocean University of China 2021年第5期20卷 1157-1166页

作者： SUN Shao’e LI Qi KONG Lingfeng Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China Laboratory for Marine Fisheries Science and Food Production Processes Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China

The mitochondrial genomes(mitogenomes)are purportedly under selection for smaller size to improve their replica-tion and translation ***,the mitogenomes of Arcidae species are larger than those of other bivalves,and are among the largest metazoan mitogenomes reported to *** order to explore the differences of base composition and selective constraints between the large and small mitogenomes,we compared the mitogenomes of 9 large arcid mitogenomes and 77 small bivalves *** composition analyses indicated that Arcidae mitogenomes have significantly greater GC skews in both their whole genomes and coding *** result suggests that the replication of the large mitogenomes in Arcidae may be slower than those in other bivalves,exposing the parental strand to deamination for a longer *** pressure analyses showed that the mitochondrial protein-coding genes of Arcidae species have significantly higher Ka/Ks ratios than other bivalves,suggesting that they have accumulated more nonsynonymous nucleotide *** protein-coding genes(atp6,cox1-3,nad1,nad4 and nad5)show significant difference for Ka/Ks ratios between the Arcidae and non-Arcidae ***,these divergences are not observed in the nuclear gene within histone *** these observations,we concluded that the large mitoge-nomes of Arcidae species experienced more relaxed selective *** some Arcidae species are more tolerant to hypoxia that can lead to low metabolic rate,the relaxed selective constraints of mitogenomes may be *** study provides new insights into the evolution of Arcidae mitogenomes.

关键词： Arcidae mitochondrial genome genome size relaxed selective constraint

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Gene characterization and phylogenetic analysis of four mitochondrial genomes in Caenogastropoda

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Acta Oceanologica Sinica 2024年第2期43卷 137-150页

作者： Jiangyong Qu Wanqi Yang Xindong Teng Li Xu Dachuan Zhang Zhikai Xing Shuang Wang Xiumei Liu Lijun Wang Xumin Wang College of Life Science Yantai UniversityYantai 264005China Qingdao International Travel Healthcare Center Qingdao 266071China Qingdao Dagang Customs Qingdao 266071China

Caenogastropoda is a highly diverse group,containing~60%of all existing *** in this subclass predominantly inhabit marine environments and have a high ecological and economic *** to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has ***,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain *** the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea *** composition analysis indicated that whole sequences were biased toward A and *** compared them with 171 complete mitochondrial genomes of *** phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close *** study supported Caenogastropoda at the molecular level as a separate clade of *** to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.

关键词： mitochondrial genome phylogenetic analysis Caenogastropoda

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