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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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The mitochondrial genome of Raphanus sativus and Gene Evolution of Cruciferous mitochondrial Types

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Journal of Genetics and Genomics 2013年第3期40卷 117-126页

作者： Shengxin Chang Jianmei Chen Yankun Wang Bingchao Gu Jianbo He Pu Chu Rongzhan Guan State Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural University Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province

To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome of Raphanus sativus （sat） was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorga-nization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type （mitotype）, together with six other re-ported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis （a representative gymnosperm）, the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames （ORFs） of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions （indets）, have resulted in the non- conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.

关键词： Radish mitochondrial genome Evolution Cruciferae

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The mitochondrial genome of the plant bug Apolygus lucorum （Hemiptera： Miridae）＂ Presently known as the smallest in Heteroptera

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Insect Science 2014年第2期21卷 159-173页

作者： Pei Wang Hu Li Ying Wang Jian-Hua Zhang Xun Dai Jian Chang Bao-Wen Hu Wan-Zhi Cai Department of Entomology China Agricultural University Beijing Research Center of Hongta Group Yuxi Yunnan China

The complete mitochondrial （mt） genome of the plant bug, Apolygus lucorum, an important cotton pest, has been sequenced and annotated in this study. The entire circular genome is 14 768 bp in size and represents the smallest in presently known heteropteran mt genomes. The mt genome is encoding for two ribosomal RNA （rRNA） genes, 22 transfer RNA （tRNA） genes, 13 protein coding genes and a control region, and the order, content, codon usage and base organization show similarity to a great extent to the hypothetical ancestral model. All protein coding genes use standard initiation codons ATN. Conventional stop codons TAA and TAG have been assigned to the most protein coding genes; however, COIII, ND4 and ND5 genes show incomplete terminator signal （T）. All tRNA genes possess the typical clover leaf structure, but the dihydrouridine arm of tRNAser（A6N） only forms a simple loop. Secondary structure models of rRNA genes are generally in accordance with the former models, although some differences exist in certain parts. Three intergenic spacers have never been found in sequenced mt genomes of Heteroptera. The phylogenetic study based on protein coding genes is largely congruent with previous phylogenetic work. Both Bayesian inference and maximum likelihood analyses highly support the sister relationship ofA. lucorum and Lygus lineolaris, and Miridae presents a sister position to Anthocoridae.

关键词： Apolygus lucorum Cimicomorpha Miridae mitochondrial genome phylo-genetic relationship secondary structure

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Structural and Expressional Variations of the mitochondrial genome Conferring the Wild Abortive Type of Cytoplasmic Male Sterility in Rice

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Journal of Integrative Plant Biology 2007年第6期49卷 908-914页

作者： Zhen-Lan Liu Hong Xu Jing-Xin Guo Yao-Guang Liu Key Laboratory of Plant Functional Genomics and Biotechnology of Education Department Guangdong Province College of Life Sciences South China Agricultural University Guangzhou 510642 China

The so-called ＂wild abortive＂（WA） type of cytoplasmic male sterility （CMS） derived from a wild rice species Oryza rufipogon has been extensively used for hybrid rice breeding. However, extensive analysis of the structure of the related mitochondrial genome has not been reported, and the CMS-associated gene（s） remain unknown. In this study, we exploited a mitochondrial genome-wide strategy to examine the structural and expressional variations in the mitochondrial genome conferring the CMS. The entire mitochondriai genomes of a CMS-WA line and two normal fertile rice lines were amplified by Long-polymerase chain reaction into tilling fragments of up to 15.2 kb. Restriction and DNA blotting analyses of these fragments revealed that structural variations occurred in several regions in the WA mitochondrial genome, as compared to those of the fertile lines. All of the amplified fragments covering the entire mitochondrial genome were used as RNA blot probes to examine the mitochondriai expression profile among the CMS-WA and fertile lines. As a result, only two mRNAs were found to be differentially expressed between the CMS-WA and the fertile lines, which were detected by a probe containing the nad5 and orf153 genes and the other having the ribosomal protein gene rpl5, respectively. These mRNAs are proposed to be the candidates for further identification and functional studies of the CMS gene.

关键词： cytoplasmic male sterility mitochondrial genome rice transcription.

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Characterization of the Complete mitochondrial genome of the Hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂,and Phylogenetic Analysis in Subfamily Epinephelinae

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Journal of Ocean University of China 2017年第3期16卷 555-563页

作者： GAO Fengtao WEI Min ZHU Ying GUO Hua CHEN Songlin YANG Guanpin College of Marine Life Science Ocean University of China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences (CAFS)Key Laboratory for Sustainable Development of Marine FisheriesMinistry of Agriculture Wuxi Fisheries College Nanjing Agricultural University

This study presents the complete mitochondrial genome of the hybrid Epinephelus moara♀× Epinephelus lanceolatus♂. The genome is 16886 bp in length, and contains 13 protein-coding genes, 2 r RNA genes, 22 t RNA genes, a light-strand replication origin and a control region. Additionally, phylogenetic analysis based on the nucleotide sequences of 13 conserved protein-coding genes using the maximum likelihood method indicated that the mitochondrial genome is maternally inherited. This study presents genomic data for studying phylogenetic relationships and breeding of hybrid Epinephelinae.

关键词： Epinephelus moara♀× Epinephelus lanceolatus♂ mitochondrial genome phylogenetic analysis

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Study on the mitochondrial genome of Sea Island Cotton(Gossypium barbadense) by BAC Library Screening

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Journal of Integrative Agriculture 2014年第5期13卷 945-953页

作者： SU Ai-guo LI Shuang-shuang LIU Guo-zheng LEI Bin-bin KANG Ding-ming LI Zhao-hu MA Zhi-ying HUA Jin-ping Key Laboratory of Crop Heterosis and Utilization Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology China Agricultural University College of Agronomy Hebei Agricultural University

The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility （CMS）. Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton （Gossypium barbadense） based on positive clones from the bacterial artificial chromosome （BAC） library. Thirty-five primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and verified for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be amplified, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

关键词： Gossypium barbadense BAC library mitochondrial genome RNA editing

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Comparative analysis of mitochondrial genome of a deepsea crab Chaceon granulates reveals positive selection and novel genetic features

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Journal of Oceanology and Limnology 2020年第2期38卷 427-437页

作者： ZHANG Bo WU Yingying WANG Xin JIANG Wei YIN Jianping LIN Qiang Key Laboratory of Tropical Marine Bio-Resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510275China Institution of South China Sea Ecology and Environmental Engineering Chinese Academy of SciencesGuangzhou 510275China University of Chinese Academy of Sciences Beijing 100049China Beijing Advanced Sciences and Innovation Center of Chinese Academy of Sciences Beijing 100049China Institute of Oceanology Chinese Academy of SciencesQingdao 266071China

Deep-sea organisms survive in an extremely harsh *** must be some genetic adaptation mechanisms for *** systematically characterized and compared the complete mitochondrial genome(mitogenome)of a deep-sea crab(Chaceon granulates)with those of shallow *** mitogenome of the crab was 16126 bp in length,and encoded 37 genes as most of a metazoan mitogenome,including 13 protein-coding genes(PCGs),22 transfer RNA(tRNA)genes,and 2 ribosomal RNA(rRNA)*** gene arrangement and orientation was conserved in the ***,a unique mitogenome element regulator,the origin of light-strand replication(O L),was firstly predicted in the present crab *** addition,further positive selection analysis showed that two residues(33 S in ND3 and 502 I in ND5)in *** mitogenome were positively selected,indicated the selective evolution of the deep-sea ***,the mitogenome of deep-sea *** showed a unique OL element and positive *** special features would influence the mitochondrial energy metabolism,and be involved in the adaptation of deepsea environment,such as oxygen deficits and low temperatures.

关键词： deep-sea organisms mitochondrial genome adaptation Chaceon granulates

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Preliminary analysis of the mitochondrial genome evolutionary pattern in primates

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Zoological Research 2012年第4期33卷 47-56页

作者： Liang ZHAO Xingtao ZHANG Xingkui TAO Weiwei WANG Ming LI Faculty of Biology Suzhou UniversitySuzhou Anhui 234000China Institute of Zoology the Chinese Academy of SciencesBeijing 100101China

Since the birth of molecular evolutionary analysis,primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique ***,to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of ***,we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from *** results revealed that a strong rate heterogeneity occurred among sites and genes in all ***,an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding *** 13 protein-coding genes,the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence,while synonymous changes differed only for individual genes,indicating that the rate heterogeneity may result from the rate of change at nonsynonymous *** usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes,and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage *** tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene,consistent with near *** tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate ***,with the exception of rate heterogeneity among mitochondrial genes,evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.

关键词： mitochondrial genome Evolutionary pattern Codon usage bias Complete linkage Evolution neutrality Primates

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Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus(Crustacea:Decapoda:Caridea):Gene rearrangement and phylogeny within Caridea

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Science China(Life Sciences) 2012年第7期55卷 591-598页

作者： SHEN Xin LI Xiao SHA ZhongLi YAN BinLun XU QiHua Jiangsu Key Laboratory of Marine Biotechnology Huaihai Institute of Technology Lianyungang 222005 China Institute of Oceanology Chinese Academy of Sciences Qingdao 266071 China Shandong Peanut Research Institute Qingdao 266100 China

The complete sequence of the mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus Miers （Crustacea： Decapoda： Caridea） is presented here. A comparative analysis based on the currently available mitochondrial genomic data re- vealed many previously unknown characteristics of the mitochondrial genomes of caridean shrimps. The A. japonicus mito- chondrial genome is 16487 bp long and contains the typical set of 37 metazoan genes. The gene arrangements in the mito- chondrial genomes of four previously studied carideans （Macrobrachium rosenbergii, M. nipponense, M. lanchesteri and Halocaridina rubra） were found to be identical to the pancrustacean ground pattern; thus, it was considered that gene rear- rangements probably did not occur in the suborder Caridea. In the present study, a translocation of the trnE gene involving in- version was found in Alpheus mitochondrial genomes. This phenomenon has not been reported in any other crustacean mito- chondrial genome that has been studied so far; however, the translocation of one transfer RNA gene （trnP or trnT） was report- ed in the mitochondrial genome of Exopalaemon carinicauda. When the ratios of the nonsynonymous and synonymous sub- stitutions rates （Ka/Ks） for the 13 protein coding genes from two Alpheus species （A. japonicus and A. distinguendus） and three Macrobrachium species （M. rosenbergii, M. nipponense, M. lanchesteri） were calculated, the KaIKs values for all the protein coding genes in Alpheus and Macrobrachium mitochondrial genomes were found to be less than 1 （between 0.0048 and 0.2057）, indicating that a strong purification selection had occurred. The phylogenetic tree that was constructed based on the mitochondrial protein coding genes in the genomes of nine related species indicated that Palaemonidae and Alpheidae formed a monophyly and shared a statistically significant relationship, （Palaemonidae＋Alpheidae）＋Atyidae, at the family level.

关键词： Decapoda Caridea mitochondrial genome gene order 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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