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Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia

Journal of Genetics and Genomics 2024年第1期51卷 87-95页

作者： Liu Yang Xing Zhang Yaning Hu Piao Zhu Hua Li Zhenyu Peng Hai Xiang Xinying Zhou Xingbo Zhao National Engineering Laboratory for Animal Breeding Key Laboratory of AnimalGeneticsBreeding and ReproductionMinistry of Agriculture and Rural AffairsCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and EngineeringFoshan UniversityFoshanGuangdong 528225China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China Key Laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China

Sheep have been one of the most important groups of animals since ancient ***,the knowledge of their migration routes and genetic relationships is still poorly *** investigate sheep maternal migration histories alongside Eurasian communications routes,in this study,we obtain mitochondrial genomes(mitogenomes)from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429–3100 years before present(BP).By obtaining the mitogenomes from the sheep(4429–3556 BP)found in the Tongtian Cave site in Xinjiang,Altai region of northwest China,our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429–3556 *** combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern *** least two migration events have taken place for sheep crossing Eurasia to China,one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 ***,this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.

关键词： Sheep Ancient DNA Eastern Asia mitochondrial genome Migration Altai

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mitochondrial genome sequencing with short overlapping amplicons on MiSeq FGx system

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Forensic Sciences Research 2022年第2期7卷 142-153页

作者： Yang Xin Rulin Jia Suhua Zhang Fei Guo Shanghai Key Laboratory of Forensic Medicine Shanghai Forensic Service PlatformAcademy of Forensic ScienceMinistry of JusticeShanghaiChina Forensic Science College Criminal Investigation Police University of ChinaShenyangChina

With the development and maturation of massively parallel sequencing(MPS)technology,the mitochondrial genome(mitogenome)sequencing is increasingly applied in the forensic *** this study,we employed the strategy of short overlapping amplicons for the whole mitogenome,library preparation with tagmentation using the Nextera®XT DNA Library Preparation Kit,sequencing on the MiSeq FGxTM Forensic Genomics System and analyzing data using the mitochondrial(mtDNA)MSR Plug-in and the mtDNA Variant Analyzer.A total of 27 libraries and 56 libraries were sequenced in a run using MiSeq Reagent Kit v2 and v3,*** showed more than 1800×of averaged depth of coverage(DoC)at each *** haplotypes of 9947 A and 2800 M were obtained at 32 ***-reactivity was observed with 1 ng primate DNA and 10 ng non-primate DNA but could be easily *** and accurate variants were obtained from at least 50 pg input DNA and from minor contributors between 19:1 and 1:19 mixed ratios with known reference *** than 86%variants were detected from≥200-bp degraded samples but its haplotype was assigned to more ancestral ***,a total of 3962 variants were observed at 613 nucleotide positions from 103 Xibe mitogenomes with 25:1 ratio of transitions to *** new transversions(C13735A and A14755C)and two tri-alleles at nps 9824 and 16092 were *** were 103 unique mitogenome haplotypes from 103 Chinese Xibe that were assigned to 79 *** D was the preponderant top-level haplogroup in Xibe followed by F,B,M,A,N,G,C,Z,Y,HV and *** match probability(RMP)and haplotype diversity(HD)of the whole mitogenome was calculated as 0.0097 and 1.0000,*** with HVS-I only,RMP decreased 33.56%,while the number of haplotypes and HD increased 15.73%and 0.49%,*** component analysis(PCA)showed that Xibe was clustered to East and Southeast *** a whole,this MPS strategy i

关键词： Forensic sciences massively parallel sequencing MiSeq FGx system mitochondrial genome Xibe degraded samples

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Assembly and analysis of the Populus deltoides mitochondrial genome:the first report of a multicircular mitochondrial conformation for the genus Populus

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Journal of Forestry Research 2023年第3期34卷 717-733页

作者： Yanshu Qu Pengyan Zhou Chunfa Tong Changwei Bi Li’an Xu Key Laboratory of Forestry Genetics&Biotechnology of Ministry of Education Co-Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjing 210037People’s Republic of China College of Information Science and Technology Nanjing Forestry UniversityNanjing 210037People’s Republic of China

Genomics research of Populus deltoides,an important timber species that is widely planted worldwide,is an important part of poplar ***,the nuclear and chloroplast genome of *** have been sequenced,but its mitochondrial genome(mitogenome)has not been *** further explore the evolution and phylogeny of ***,the mitogenome of *** I-69 was assembled using reads from Nanopore and Illumina sequencing platforms and found to consist of 802,637 bp and three circular chromosomes(336,205,280,841,and 185,591 bp)containing 58 genes(34 protein-coding genes,21 tRNA genes,and 3 rRNA genes).RNA analysis in combination with several species showed signifi cantly fewer RNA editingsites in the mitogenomes of poplar and other angiosperms than in *** transfer analysis showed extensive mitogenome rearrangements in Populus species,and with evolution from lower to higher plants,tRNA transfer from chloroplasts to mitochondria became increasingly *** a phylogenetic analysis,the evolutionary status of *** was determined,and the section Populus was *** results based on the fi rst report of a multicircular conformation of the Populus mitogenome provide a basis for further study of the evolution and genetics of *** and other Populus species and for breeding programs.

关键词： mitochondrial genome Multi-circular Populus deltoids Comparative genomics Phylogeny

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Insight into the characteristics of an important evolutionary model bird(Geospiza magnirostris)mitochondrial genome through comparison

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BIOCELL 2022年第7期46卷 1733-1746页

作者： ZHENGGANG XU LIANG WU JIAHAO CHEN YUNLIN ZHAO CHONGXUAN HAN TIAN HUANG GUIYAN YANG Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster College of ForestryNorthwest A&F UniversityYangling712100China Engineering Research Center for Internet of Animals Changsha410000China Key Laboratory of Forestry Remote Sensing Based Big Data&Ecological Security for Hunan Province Central South University of Forestry and TechnologyChangsha410004China

Darwin’s finches are the most classic case of *** studies on the evolution of this species were mainly based on *** now,the mitochondrial genome of Geospiza magnirostris has been sequenced and the study explored the characteristics of the complete genome of *** and verified the evolutionary position of *** 13 PCGs initiated by ATN *** stop codons of three PCGs(ND2,COX3 and ND4)were incomplete,with only T-or TA-replacing complete form TAA or *** the tRNA genes expressed a typical cloverleaf secondary structure,except for tRNA^(Ser1)(AGY),whose dihydrouridine(DHU)arm was lack and instead with a simple *** the sequence of the control region of ***,we found six simple repeat tandem sequences with a total length of 42 *** characteristic conserved overlapping junction(ATGCTAA)and(CAAGAAAG)were observed as reported for eight selected Passeriformes birds.A special conserved overlapping junction(ATCTTACC)involved in mitochondrial transcription termination was found between tRNA^(Tyr) and COX1 in ***’s control *** most frequently used amino acids in ***’s PCGs were Leu1(CUN),Ile,Thr,*** codon usage of *** was relatively average,and there was no particular *** ratio Ka/Ks results showed that *** receives less natural selection *** phylogenetic relationships and cluster analysis of relative codon usage showed that *** and Thraupis episcopus clustered in one *** phylogenetic position of *** was consistent with the traditional taxonomic of *** results supported the conclusion that *** belongs to the morphological classification of the family Thraupidae.

关键词： Geospiza magnirostris mitochondrial genome Comparative analysis Evolution analysis Phylogenetic relationships

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Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement

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Zoological Systematics 2022年第4期47卷 293-304页

作者： Qingsong Zhou Mei Xiong Arong Luo Xubo Wang San’an Wu Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101China College of Biological Sciences University of Chinese Academy of SciencesBeijing 100049China Southwest Forestry University Kunming 650224China The Key Laboratory for Silviculture and Conservation of Ministry of Education Beijing Forestry UniversityBeijing 100083China

Scale insects comprise a diverse group of insects within superfamily Coccoidea in the suborder Sternorrhyncha,many of them are important pests of economic *** advent in next-generation sequencing(NGS)technologies has revolutionized conventional phylogenomic researches,causing a rapid accumulation of sequenced insect mitochondrial ***,there have been few studies on the mitochondrial genome of diverse scale insect *** using NGS methods,the complete mitochondrial genome of Nipponaclerda biwakoensis was obtained in this study,representing the first mtDNA of the family *** whole mitochondrial genome is 16,654 bp in length with an A+T content of 81.3%,including 13 protein-coding genes(PCGs),2 ribosomal RNAs,17 transfer RNAs and a control *** PCGs begin with typical ATN codons and use standard TAA as their termination codons,except nad1 gene stopping with ***,this mitochondrial genome shows a unique gene rearrangement with a long fragment(trnP-trnC-trnI-nad2-trnY-trnT)insertion in the conserved region nad6-cob,which is novel to Hemiptera,even *** phylogeny reconstruction of Sternorrhyncha based on 13 PCGs and 2 rRNAs under Bayesian Inference method support a robust topology that Aleyrodoidea is the earliest branch of Sternorrhyncha,with Psylloidea as the sister group of the(Aphidoidea+Coccoidea)clade.

关键词： mitochondrial genome scale insects gene arrangement phylogeny Nipponaclerda biwakoensis

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Characterization of Rheum palmatum mitochondrial genome and comparative analysis among Caryophyllales species

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Acupuncture and Herbal Medicine 2023年第4期3卷 323-332页

作者： Longlong Gao Lijun Hao Wenjie Xu Tianyi Xin Chi Song Yulin Lin Lingping Zhu Jingyuan Song Key Lab of Chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of the People’s Republic of ChinaEngineering Research Center of Chinese Medicine Resource of Ministry of EducationInstitute of Medicinal Plant DevelopmentPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina Institute of Herbgenomics State Key Laboratory of Southwest Chinese Medicine ResourcesPharmacy CollegeChengdu University of Traditional Chinese MedicineChengduChina

Objective:This work aimed to report the first complete mitochondrial genome(mitogenome)of Rheum palmatum,summarize the features of Caryophyllales mitogenomes,and to reveal the potential of utilizing the mitogenomes of *** and other Caryophyllales species for inferring phylogenetic relationships and species ***:Both Illumina short reads and PacBio HiFi reads were utilized to obtain a complete mitogenome of ***.A variety of bioinformatics tools were employed to characterize the *** mitogenome,compare the reported mitogenomes in Caryophyllales and conduct phylogenetic ***:The mitogenome of *** was assembled into a single master circle of 302,993 bp,encoding 35 known protein-coding genes,18 transfer RNA genes,and three ribosome RNA genes.A total of 249 long repeats and 49 simple sequence repeats were identified in this *** sizes of mitogenomes in Caryophyllales varied from 253 kb to 11.3 *** them,23 mitogenomes were circular molecules,one was linear,and one consisted of relaxed circles,linear molecules,and supercoiled *** of the total mitogenomes,11 were single-chromosome structure,whereas the remaining 14 were multi-chromosomal *** phylogenetic analysis is consistent with both the Engler system(1964)and the Angiosperm Phylogeny Group III ***:We obtained the first mitogenome of ***,which consists of a master *** in Caryophyllales have variable genome sizes and structures even within the same *** molecules are still the dominant pattern in ***-chromosome mitogenomes account for nearly a half of all the mitogenomes in Caryophyllales,in contrast to previous *** is feasible to utilize mitochondrial genomes for inferring phylogenetic relationships and conducting species identification.

关键词： Caryophyllales mitochondrial genome Molecular identification Phylogenetic analysis Rheum palmatum

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mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana:assessing molecular changes for high plateau adaptation

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Science China Life Sciences 2013年第5期56卷 440-452页

作者： ZHANG HangXiao LUO QiBin SUN Jing LIU Fei WU Gang YU Jun WANG WeiWei CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences Department of genome Oriented Bioinformatics Technische Universit t MünchenWissenschaftszentrum WeihenstephanFreising 85350Germany Division of Gastroenterology Department of MedicineUniversity of AlbertaEdmonton T6G 2V2AlbertaCanada

Brine shrimps,Artemia(Crustacea,Anostraca),inhabit hypersaline environments and have a broad geographical distribution from sea level to high *** therefore possess significant genetic diversity,which gives them their outstanding *** understand this remarkable plasticity,we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia,*** compared the ratio of the rate of nonsynonymous(Ka) and synonymous(Ks) substitutions(Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of *** with either *** or *** and that atp6 had the highest Ka/Ks ratio between *** and ***6 may have experienced strong selective pressure for high-altitude adaptation because although *** and *** are closely related they live at different *** identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial *** propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes.

关键词： mitochondrial genome Artemia tibetiana sequence variation high plateau species

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The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

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Journal of Genetics and Genomics 2008年第1期35卷 33-40页

作者： Li Zhang Liuwang Nie Chenghe Cao Ying Zhang College of Life Sciences Anhui Normal University the Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui Wuhu 241000 China

The complete mitochondrial genome （16,837 bp） from the Keeled box turtle （Pyxidea mouhotii） was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule： a large number of （ATTATATC） n direct tandem repeats followed by （TA） n microsatellite at the 3＇ end of the control region （D-loop）, which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood （ML） and Bayesian （BI） analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1） Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group （containing Pyxidea） may have originated from two ancestors; 2） the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.

关键词： Pyxidea mouhotii mitochondrial genome control region phylogenetic relationships

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Complete mitochondrial genome of the Steppe Ribbon Racer(Psammophis lineolatus):The First Representative from the Snake Family Psammophiidae and its Phylogenetic Implications

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Asian Herpetological Research 2021年第3期12卷 295-307页

作者： Minli CHEN Jinlong LIU Jun LI Na WU Xianguang GUO Chengdu Institute of Biology Chinese Academy of SciencesChengdu 610041SichuanChina University of Chinese Academy of Sciences Beijing 100049China College of Life Science and Technology Xinjiang UniversityUrumqi 830046XinjiangChina

Comparisons of vertebrate mitochondrial genomes(mitogenomes)may yield significant insights into the evolution of organisms and ***,no complete mitogenome from the snake family Psammophiidae has been *** this study,we sequenced and annotated the complete mitogenome of Psammophis lineolatus,representing the first mitogenome of *** total length is 17166 bp,consisting of 13 protein-coding genes(PCGs),22 transfer RNAs(tRNAs),two ribosomal RNAs(12 S rRNA and16 S rRNA),and duplicate control regions(CRs).This gene arrangement belongs to the TypeⅢpattern,which is a widely shared gene order in Alethinophidian *** tRNAs exhibit cloverleaf structures with the exception of tRNA-Ser^(AGY) and tRNA-Pro,which lack a dihydrouridine(DHU)arm/stem and TΨC loop,*** 13 PCGs include five start codons(ATG,GTG,ATA,ATT,and ATC),two complete stop codons(TAA and AGG),and two incomplete stop codon(T--and TA-).In addition,the Ka/Ks ratios indicate that all PCGs had undergone a strong purifying *** types of CR domains rearrangement occurred among eight species of *** phylogenetic reconstructions with both Bayesian inference and maximum likelihood methods support the placement of Psammophiidae in the Elapoidea superfamily,with Homalopsidae being the sister taxon to Elapoidea and ***,the sister taxon of Psammophiidae is unclear due to the availability of Elapoidea mitogenomes being limited to the family *** mitogenomes from different taxonomic groups in Elapoidea are needed to better understand the phylogenetic relationships within Elapoidea.

关键词： mitochondrial genome phylogenetic relationships Psammophis lineolatus Psammophiidae purifying selection

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The complete mitochondrial genome of the grey bamboo shark (Chiloscyllium griseum) (Orectolobiformes: Hemiscylliidae): genomic characterization and phylogenetic application

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Acta Oceanologica Sinica 2013年第4期32卷 59-65页

作者： CHEN Xiao AI Weiming YE Le WANG Xuehui LIN Chongwen YANG Shengyun College of Fisheries Ocean University of China Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-Resource Zhejiang Mariculture Research Institute Department of Marine Science School of Life Science Wenzhou Medical College South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Laboratory of Marine Biodiversity and Global Change College of Ocean and Earth Sciences Xiamen University

The complete mitochondrial genome of the grey bamboo shark, Chiloscyllium griseum （Orectolobiformes： HemiscyUiidae） was obtained, with a total of 16 755 base pairs （bp）. The mitogenome encoded 13 protein- coding genes, two ribosomal RNAs, 22 transfer RNAs and a noncoding control region, a gene arrangement identical to the most common type found in vertebrates. All tRNA sequences were folded into typical clover- leaf secondary structure with the exception of tRNA-Ser2, in which the DHU arm stem was replaced with 12 unpaired nucleotides and formed a simple loop. In the control region, the putative termination-associated sequences （TAS） with hairpin-loop structure and the conserved sequence blocks （CSB） I-III were identified and considered to be associated with the replication and transcription of mtDNA. No repeat motifs were found in the mitogenome of C. griseum. On the basis of the mitogenomic data available in the Class Chon- drichthyes from both Genbank and this study, and the phylogenetic analyses using maximum likelihood （ML） and Bayesian inference （BI） methods, the results strongly support the basal division between batoids and sharks and the monophyly of the Superorder Galeomorphii, and confirm the phylogenetic position of C. griseum in the Subclass Elasmobranchii. This study suggests that the mitogenomic data are more robust for reconstructing phylogenetic relationships than individual genes in the Elasmobranchii.

关键词： mitochondrial genome Chiloscyllium griseum Chondrichthyes phylogeny carpet shark,Galeomorphii

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