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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

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

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

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

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

The complete mitochondrial genome of the hybrid grouper Epinephelus moara(♀)×Epinephelus tukula(♂), and phylogenetic analysis in subfamily Epinephelinae

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Acta Oceanologica Sinica 2020年第12期39卷 65-75页

作者： Zhentong Li Yongsheng Tian Meiling Cheng Linna Wang Jingjing Zhang Yuping Wu Zunfang Pang Wenhui Ma Jieming Zhai College of Fisheries and Life Science Shanghai Ocean UniversityShanghai 201306China Laboratory for Marine Fisheries Science and Food Production Processes Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266071China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery SciencesQingdao 266071China College of Fisheries and Life Science Dalian Ocean UniversityDalian 116023China Laizhou Mingbo Aquatic Co.Ltd. Laizhou 261400China

The mitochondrial genome(mitogenome)of hybrid grouper Epinephelus moara(♀)×Epinephelus tukula(♂),a new hybrid progeny,can provide valuable information for analyzing phylogeny and molecular *** this study,the mitogenome was analyzed using PCR amplification and sequenced,then the phylogenetic relationship of ***(♀)×***(♂)and 35 other species were constructed using Maximum Likelihood and NeighborJoining methods with the nucleotide sequences of 13 conserved protein-coding genes(PCGs).The complete mitogenome of ***(♀)×***(♂)was 16695 bp in length,which contained 13 PCGs,2 rRNA genes,22 tRNA genes,a replication origin and a control *** composition and order of these genes were consistent with most other *** the 13 PCGs,12 PCGs were encoded on the heavy strand,and ND6 was encoded on the light *** mitogenome of the ***(♀)×***(♂)had a higher AT nucleotide content,a positive AT-skew and a negative *** protein initiation codons were ATG,except for COX and ND4(GTG),ATP6(CTG),and ND3(ATA).ND2,COXII,ND3,ND4 and Cytb had T as the terminating codon,COXIII’s termination codon was TA,and the remaining PCGs of that were *** tRNA genes,except for the lacking DHU-arm of tRNASer(AGN),were predicted to form a typical cloverleaf secondary *** addition,sequence similarity analysis(99%identity)and phylogenetic analysis(100%bootstrap value)indicated that the mitochondrial genome was maternally *** study provides mitogenome data for studying genetic,phylogenetic relationships and breeding of grouper.

关键词： Epinephelus moara(♀)×Epinephelus tukula(♂) Epinephelus moara Epinephelus tukula mitochondrial genome phylogeny

Characterization of the Complete mitochondrial genome of Arius dispar(Siluriformes: Ariidae) and Phylogenetic Analysis Among Sea Catfishes

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Journal of Ocean University of China 2020年第5期19卷 1198-1206页

作者： CUI Lei DONG Yuelei CAO Rongbo ZHOU Xiaoyu LU Songhui Research Center of Harmful Algae and Marine Biology Jinan UniversityGuangzhou 510632China Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes Jinan UniversityGuangzhou 510632China Southern Marine Science and Engineering Guangdong Laboratory Zhuhai 519000China

The mitochondrial genome(mitogenome) was 16792 bp in length, containing 13 protein coding genes(PCGs), two rRNA genes(12 S rRNA and 16 S rRNA), 22 tRNA genes, and two main non-coding regions. Among these 37 genes, 28 genes were encoded on the heavy strand, while 9 genes were transcribed on the light strand. The non-coding regions of A. dispar included a control region, a light strand replication and another 11 intergenic spacers. The CR of A. dispar contained 8 conserved sequence blocks(CSBs), a termination-associated sequence(TAS) and a pyrimidine tract. Phylogenetic analysis based on 12 PCGs revealed that A. dispar was genetically closest to Arius arius. The families Schilbeidae, Claroteidae, Mochokidae, and Ariidae formed a closely evolved clade. Molecular information from this research introduces mitogenomice data of A. dispar and suggests the phylogenetic relationships among Siluriformes.

关键词： mitochondrial genome Siluriformes Ariidae Arius dispar phylogeny

The complete mitochondrial genome of Anopheles minimus （Diptera： Culicidae） and the phylogenetics of known Anopheles mitogenomes

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Insect Science 2016年第3期23卷 353-365页

作者： Ya-Qiong Hua Yi-Ran Ding Zhen-Tian Yan Feng-Ling Si Qian-Chun Luo Bin Chen Institute of Entomology and Molecular Biology College of Life Sciences Chongqing Normal University Chongqing China

Anopheles minimus is an important vector of human malaria in southern China and Southeast Asia. The phylogenetics of mosquitoes has not been well resolved, and the mitochondrial genome （mtgenome） has proven to be an important marker in the study of evolutionary biology. In this study, the complete mtgenome of An. minimus was sequenced for the first time. It is 15 395 bp long and encodes 37 genes, including 13 protein-coding genes （PCGs）, 22 transfer RNAs （tRNAs）, two ribosomal RNAs （rRNAs） and a non-coding region. The gene organization is consistent with those of known Anopheles mtgenomes. The mtgenome performs a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All 13 PCGs prefer to use the codon UUA （Leu）, ATN as initiation codon but cytochrome-oxidase subunit 1 （COI） and ND5, with TCG and GTG, and TAA as termination codon, but COI, COII, COIII and ND4, all with the incomplete T. tRNAs have the typical clover-leaf structure, but tRNAser^a~N） is consistent with known Anopheles mtgenomes. The control region includes a conserved T-stretch and a （TA）n stretch, and has the highest A＋T content at 93.1%. The phylogenetics of An. minimus with 18 other Anopheles species was constructed by maximum likelihood and Bayesian inference, based on concatenated PCG sequences. The subgenera, Cellia and Anopheles, and Nyssorhynchus and Kerteszia have mutually close relationships, respectively. The Punctulatus group and Leueosphyrus group of Neomyzomyia Series, and the Albitarsis group of Albitarsis Series were suggested to be monophyletic. The monophyletic status of the subgenera, Cellia, Anopheles, Nyssorhynchus and Kerteszia need to be further elucidated.

关键词： Anopheles minimus Anopheles mitochondrial genome phylogeneticanalysis

The mitochondrial genome of Chaeturichthys stigmatias provides novel insight into the interspecific difference with Amblychaeturichthys hexanema

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Acta Oceanologica Sinica 2021年第9期40卷 74-81页

作者： Jian Zheng Bingjie Chen Tianxiang Gao Na Song Key Laboratory of Mariculture of Ministry of Education Ocean University of ChinaQingdao 266003China Fishery College Zhejiang Ocean UniversityZhoushan 316022China

Chaeturichthys stigmatias and Amblychaeturichthys hexanema belong to the family Gobiidae,which are offshore warm fish species and widely distribute in the western Pacific *** this study,the mitochondrial cytochrome c oxidase subunit I(COI)sequences and 12 S ribosomal RNA(12 S rRNA)sequences were used to analyze the interspecific differences between the two *** phylogenetic analysis showed that the interspecific distance was significantly higher than the intraspecific genetic *** Neighbor-Joining tree showed two separate clusters,without sharing *** mitochondrial genome sequence of *** was also *** genome was 17134 bp in size,with a high A+T content of 55.9%.The phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences indicated that *** showed a close relationship with *** study can provide the basic genetic data for two species and will help for constructing the phylogeny of the Gobiiade.

关键词： Chaeturichthys stigmatias Amblychaeturichthys hexanema mitochondrial genome phylogenetic analysis