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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4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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Complete mitochondrial genome of Ampittia dioscorides （Lepidoptera： Hesperiidae） and its phylogenetic analysis

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Frontiers in Biology 2017年第1期12卷 71-81页

作者： Xin-Min Qin Xiao-Wen Yang Li-Xia Hou Hui-Min Li Guangxi Key Laboratory of Rare and Endangered Animal Ecology College of Life Science Guangxi Normal UniversityGuilin 541004 China

The complete mitochondrial genome of Ampittia dioscorides （Lepidoptera： Hesperiidae） was determined. The sequenced genome is a circular molecule of 15313 bp, containing 13 protein-coding genes （PCGs）, 22 tRNA genes, two rRNA genes, and an A ＋ T-rich region. The gene arrangements and transcribing directions are identical to those in most of the reported lepidopteran mitogenomes. The base composition of the whole genome and genes or regions are also similar to those in other lepidopteran species. All the PCGs are initiated by typical ATN codons; the exception being CO1, which begins with a CGA codon. Eight genes （ND2, ATPase8, ATPase6, COIII, ND5, ND4L, ND6, and Cytb） end with a TAA stop codon, and two genes （ND1 and ND3） end with TAG. The remaining three genes （CO1 and COIl, which end with TA-, and ND4, which ends with T-） have incomplete stop codons. All tRNAs have the typical clover-leaf structure of mitochondrial tRNAs, with the exception of tRNAser（AGY）. On the basis of the concatenated nucleotide and amino acid sequences of the 13 PCGs and wingless gene of 22 butterfly species, maximum parsimony （MP） and Bayesian inference （BI） trees were constructed, respectively. Both MP and BI trees had the same topological structure：（（（（Nymphalidae ＋ Danaidae）＋ Lycaenidae）＋ Pieridae）＋ Papilionidae）＋ Hesperiidae）. The results provide support for Hesperiidae as a superfamily-level taxon.

关键词： Ampittia dioscorides mitochondrial genome phylogeny

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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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A mitochondrial genome Sequence of the Tibetan Antelope(Pantholops hodgsonii)

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Genomics, Proteomics & Bioinformatics 2005年第1期3卷 5-17页

作者： Shu-Qing Xu Ying-Zhong Yang Jun Zhou Guo-En Jing Yun-Tian Chen Jun Wang Huan-Ming Yang Jian Wang Jun Wu Xiao-Guang Zheng and Ri-Li Ge Beijing Genomics Institute Chinese Academy of Sciences Beijing 101300 China Research Center forHigh Altitude Medicine Qinghai University Xining 810016 China Kunming Institute of Zoology ChineseAcademy of Sciences Kunming 650223 China Graduate School Chinese Academy of Sciences Beijing100049 China.

To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis ames and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii （16,498 bp） revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. ames and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. ames and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. ames is about 2.25 million years ago. Eutther analysis on natural selection indicated that the COXI （cytochrome c oxidase subunit I） gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.

关键词： tibetan antelope mitochondrial genome adaptation COXI

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Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis(McLachlan)(Insecta:Megaloptera:Corydalidae)

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动物分类学报 2014年第2期39卷 209-223页

作者： Yi-Ran Wang Yu-Yu Wang Wen-Cheng Chang Xing-Yue Liu Ding Yang Department of Entomology China Agricultural University

The complete mitochondrial genome of Acanthacorydalis orientalis （McLachlan） was determined and analyzed （GenBank accession number： KF840564）. This paper represents the first mitochondrial （mt） genome of the dobsonfly genus Acanthacorydalis. The mt genome is a typical circular DNA of 15 753 bp composed of 37 genes with an A＋T content of 76.7%. It has an ancestral gene arrangement of the insect mt genomes. Eleven of the 13 PCGs start with codon ATT and ATG,while several exceptions such as ATA and TTG respectively for atp 8 and nad 1 are also present. Five protein-coding genes end with a single T, while others have a termination codon of TAA or TAG. Most tRNAs are folded into the typical clover-leaf structure except for the trnS 1 whose dihydrouridine arm was a simple loop. The secondary structure of rrnl consists of five structural domains and 50 helices, while the rrns includes three domains and 34 helices. The control region has a stretches of Ts with a length of 22 bp but lacks obvious tandem repeat region. Both Bayesian inference and maximum likelihood （ML） analyses, based on all 13 protein-coding genes and two rRNA genes of the mt genomes, confirm the monophyly of Corydalinae and suggest that Acanthacorydalis, together with Corydalus, which is an endemic dobsonfly genus from the New World, belong to a monophyletic lineage.

关键词： Acanthacorydalis orientalis Corydalidae Megaloptera mitochondrial genome

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The first mitochondrial genome for the butterfly family Riodinidae(Abisara fylloides)and its systematic implications

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Zoological Research 2013年第5期34卷 109-119页

作者： Fang ZHAO Dun-Yuan HUANG Xiao-Yan SUN Qing-Hui SHI Jia-Sheng HAO Lan-Lan ZHANG Qun YANG College of Life Sciences Anhui Normal UniversityWuhu 24100China College of Forestry Jiangxi Environmental Engineering Vocational CollegeGanzhou 34100China Nanjing Institute of Geology and Palaeontology Chinese Academy of SciencesNanjing 21008China

The Riodinidae is one of the lepidopteran butterfly *** study describes the complete mitochondrial genome of the butterfly species Abisara fylloides,the first mitochondrial genome of the Riodinidae *** results show that the entire mitochondrial genome of *** is 15301 bp in length,and contains 13 protein-coding genes,2 ribosomal RNA genes,22 transfer RNA genes and a 423 bp A+T-rich *** gene content,orientation and order are identical to the majority of other lepidopteran *** reconstruction was conducted using the concatenated 13 protein-coding gene(PCG)sequences of 19 available butterfly species covering all the five butterfly families(Papilionidae,Nymphalidae,Peridae,Lycaenidae and Riodinidae).Both maximum likelihood and Bayesian inference analyses highly supported the monophyly of Lycaenidae+Riodinidae,which was standing as the sister of *** addition,we propose that the riodinids be categorized into the family Lycaenidae as a subfamilial taxon.

关键词： Abisara fylloides mitochondrial genome Riodinidae Systematic implication

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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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General methods to obtain and analyze the complete mitochondrial genome of aphid species: Eriosoma lanigerum(Hemiptera: Aphididae) as an example

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Zoological Systematics 2016年第2期41卷 123-132页

作者： Yuan Wang Liyun Jiang Yongjie Liu Jing Chen Gexia Qiao Shaanxi International Travel Healthcare Center Shaanxi Entry-Exit Inspection and Quarantine Bureau Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences

Insect mitochondrial （mt） genomes are of great interest in researching on molecular evolution, phylogenetics and population genetics. Aphidoidea have about more than 5 000 known species including some agricultural, forestry and horticultural pests. However, only nine complete mt genomes have been previously released in this insect group since the first one, Schizaphis graminum （Hemiptera： Aphididae： Aphidinae） in 2004. Herein, we present the complete mitochondrial genome of Eriosoma lanigerum, the first species from the subfamily Eriosomatinae. This study takes this species as an example, combing the research during past 12 years, and concludes the general methods to obtain, analyze and annotate the complete mitochondrial genome of aphid species.

关键词： mitochondrial genome Eriosoma lanigerum methods aphids

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The Complete mitochondrial genome of Salt-water Crocodile (Crocodylus porosus) and Phylogeny of Crocodilians

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Journal of Genetics and Genomics 2007年第2期34卷 119-128页

作者：李艳吴孝兵季学峰晏鹏 George Amato 安徽师范大学生命科学学院 Molecular Systematics Laboratory American Museum of Natural History New York 10024

The nucleotide sequence of the complete mitochondrial DNA （mtDNA） molecule of the salt-water crocodile （Crocodylus porosus） was determined in this article. The molecule is 16,917 base pairs Cop） in length, and codes for 22 tRNAs, 13 protein-coding genes, 2 rRNAs, as well as a control region （D-loop）, as is characteristic for mitochondrial genomes of other metazoans. The gene order conforms to that of other crocodilians sequenced, but the arrangement of some tRNA genes differs from other vertebrates. It shows that the gene order of crocodilians is remarkably conserved. In this study, the relationships among crocodilians were examined in the phylogenetic analysis based on the control conserved regions of 17 crocodilians. The results suggest that the gharial （Gavialis gangeticus） joins the false gharial （Tomistoma schlegelii） on a common branch, and then constitutes a sister group to traditional Crocodylidae. Thus, the result supports that G gangeticus belongs to Crocodylidae. The analyses also suggest that the African slender-shouted crocodile （Crocodylus cataphractus） can be treated as an isolated genus, and constitutes a sister group to Crocodylus.

关键词： Crocodylus porosus mitochondrial genome phylogeny

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Sequencing and analysis of the complete mitochondrial genome in Anopheles sinensis(Diptera:Culicidae)

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Infectious Diseases of Poverty 2017年第1期6卷 1324-1329页

作者： Kai Chen Yan Wang Xiang-Yu Li Heng Peng Ya-Jun Ma Department of Tropical Infectious Diseases Second Military Medical UniversityShanghai 200433China Department of Medical Microbiology and Parasitology Second Military Medical UniversityShanghai 200433China Team ten Cadet Brigade Second Military Medical UniversityShanghai 200433China

Background:Anopheles sinensis(Diptera:Culicidae)is a primary vector of Plasmodium vivax and Brugia malayi in most regions of *** addition,its phylogenetic relationship with the cryptic species of the Hyrcanus Group is complex and remains *** genome sequences are widely used as molecular markers for phylogenetic studies of mosquito species complexes,of which mitochondrial genome data of *** is not ***:*** samples was collected from Shandong,China,and identified by molecular *** DNA was extracted,followed by the Illumina *** complete mitochondrial genomes were assembled and annotated using the mitochondrial genome of *** as *** mitochondrial genomes sequences of the 28 known Anopheles species were aligned and reconstructed phylogenetic tree by Maximum Likelihood(ML)***:The length of complete mitochondrial genomes of *** was 15,076 bp and 15,138 bp,consisting of 13 protein-coding genes,22 transfer RNA(tRNA)genes,2 ribosomal RNA(rRNA)genes,and an AT-rich control *** in other insects,most mitochondrial genes are encoded on the J strand,except for ND5,ND4,ND4L,ND1,two rRNA and eight tRNA genes,which are encoded on the N *** bootstrap value was set as 1000 in ML *** topologies restored phylogenetic affinity within subfamily *** ML tree showed four major clades,corresponding to the subgenera Cellia,Anopheles,Nyssorhynchus and Kerteszia of the genus ***:The complete mitochondrial genomes of *** were *** number,order and transcription direction of *** mitochondrial genes were the same as in other species of family Culicidae.

关键词： Anopheles sinensis mitochondrial genome Phylogenetic relationship

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