棉铃虫膨胀线粒体基因组的鉴定与分析
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摘要
以已公布的棉铃虫线粒体DNA序列对来自4头棉铃虫雄蛹的DNA的三代测序数据进行筛选,获得了11条与线粒体DNA有同源性的三代read序列,并根据其中的read 66003鉴定出了一种膨胀的线粒体基因组。该线粒体基因组大小为27 113 bp,其保守区域包含13个蛋白编码基因、2个rRNA基因、22个tRNA基因以及1个AT富集区,与已公布的棉铃虫线粒体基因组的结构相似。膨胀区域位于cox1基因编码区内部,大小为11 467 bp,经预测含有一个完整的真核基因(依赖ATP的RNA解旋酶)以及多种转座元件的片段,但与线粒体DNA无同源性,也无I类或Ⅱ类内含子存在的证据。对田间和室内棉铃虫DNA样品的PCR扩增未能检测到膨胀线粒体基因组的存在。以上结果表明膨胀片段可能是细胞核DNA序列通过偶然的水平转移事件而整合到线粒体基因组中的,且该种膨胀方式的发生概率极低。本文报道的膨胀线粒体基因组为日后动物线粒体基因组学的研究提示了一种独特的变异方式。
BLAST search against the whole genome PacBio sequencing reads derived from four Helicoverpa armigera male pupae by using the published mitochondrial genome of this insect retrieved 11 reads, one of which, read 66003, represented an expanded mitochondrial genome of H. armigera. Its size is 27 113 bp and, like the published mitochondrial genome of H. armigera, contained all the 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one A/T-rich region in the same order. In addition, this genome contained a 11 467 bp expanded region inserting into the coding sequence of cox1. The insertion encodes a ATP-dependent RNA helicase, containing fragments of several different transposable elements but lacking group I and group Ⅱ introns. Sequence-specific PCR failed to find the presence of this expanded mitochondrial genome in multiple individuals. These results indicated that this expanded mitochondrial genome rarely occurred through a recent horizontal transfer event of nuclear DNA sequence into the normal mitochondrial genome and its frequency remained extremely low. The expanded mitochondrial genome described here represents a distinct variation of mitochondrial genome.
BLAST search against the whole genome PacBio sequencing reads derived from four Helicoverpa armigera male pupae by using the published mitochondrial genome of this insect retrieved 11 reads, one of which, read 66003, represented an expanded mitochondrial genome of H. armigera. Its size is 27 113 bp and, like the published mitochondrial genome of H. armigera, contained all the 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one A/T-rich region in the same order. In addition, this genome contained a 11 467 bp expanded region inserting into the coding sequence of cox1. The insertion encodes a ATP-dependent RNA helicase, containing fragments of several different transposable elements but lacking group I and group Ⅱ introns. Sequence-specific PCR failed to find the presence of this expanded mitochondrial genome in multiple individuals. These results indicated that this expanded mitochondrial genome rarely occurred through a recent horizontal transfer event of nuclear DNA sequence into the normal mitochondrial genome and its frequency remained extremely low. The expanded mitochondrial genome described here represents a distinct variation of mitochondrial genome.
引文
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[12] 邱忠营. 直翅目昆虫线粒体基因组比较、谱系及进化研究[D]. 西安:陕西师范大学, 2016.
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[14] SMITH D R, KAYAL E, YANAGIHARA A A, et al. First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution [J]. Genome Biology and Evolution, 2011, 4(1):52-58.
[15] SHAO Renfu, KIRKNESS E F, BARKER S C. The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus [J]. Genome Research, 2009, 19(5):904-912.
[16] LANG B F, LAFOREST M J, BURGER G. Mitochondrial introns: a critical view [J]. Trends in Genetics, 2007, 23(3):119-125.
[17] HAUSNER G. Fungal mitochondrial genomes, plasmids and introns [J]. Applied Mycology and Biotechnology,2003,3(3):101-131.
[18] BROWN G G, COLAS DES FRANCS-SMALL C, OSTERSETZER-BIRAN O. Group Ⅱ intron splicing factors in plant mitochondria [J]. Frontiers in Plant Science, 2014, 5(5):35.
[19] BEAGLEY C T, OKADA N A, WOLSTENHOLME D R. Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase [J]. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93(11):5619-5623.
[20] MEDINA M, COLLINS A G, TAKAOKA T L, et al. Naked corals: Skeleton loss in Scleractinia[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(24):9096-9100.
[21] TANG Sha, HYMAN B C. Mitochondrial genome haplotype hypervariation within the isopod parasitic nematode Thaumamermis cosgrovei [J].Genetics,2007,176(2):1139-1150.
[22] SNYDER M, FRASER A R, LAROCHE J, et al. Atypical mitochondrial DNA from the deep-sea scallop Placopecten magellanicus [J]. Proceedings of the National Academy of Sciences of the United States of America,1987,84(21):7595-7599.
[23] FULLER K M, ZOUROS E. Dispersed discrete length polymorphism of mitochondrial DNA in the scallop Placopecten magellanicus (Gmelin)[J]. Current Genetics, 1993, 23(4):365-369.
[24] SMITH D R, SNYDER M. Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome[J]. Journal of Molecular Evolution, 2007, 65(4):380-391.
[25] RIGAA A, MONNEROT M, SELLOS D. Molecular cloning and complete nucleotide sequence of the repeated unit and flanking gene of the scallop Pecten maximus mitochondrial DNA: putative replication origin features [J]. Journal of Molecular Evolution, 1995, 41(2):189-195.
[26] LIU Yunguo, KUROKAWA T, SEKINO M, et al. Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: an ultra-large metazoan mitochondrial genome [J]. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2012, 8(1):72-81.
[27] RAIMOND R, MARCADé I, BOUCHON D, et al. Organization of the large mitochondrial genome in the isopod Armadillidium vulgare [J]. Genetics, 1999, 151(1):203-210.
[28] BOYCE T M, ZWICK M E, AQUADRO C F. Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy[J]. Genetics, 1989, 123(4):825-836.
[29] YIN Jiao, HONG Guiyun, WANG Aiming, et al. Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other lepidopterans [J].Mitochondrial DNA Part A,2010,21(5):160-169.
[30] GRANT J R, STOTHARD P. The CGView Server: a comparative genomics tool for circular genomes [J]. Nucleic Acids Research, 2008, 36:w181-w184.
[31] HU Bo, JIN Jinpu, GUO Anyun, et al. GSDS 2.0: an upgraded gene feature visualization server [J].Bioinformatics, 2014, 31(8):1296-1297.
[32] KOHANY O, GENTLES A J, HANKUS L, et al. Annotation, submission and screening of repetitive elements in Repbase: Repbase Submitter and Censor [J]. BMC Bioinformatics, 2006, 7(1):474.
[33] HARTL D L. Mitochondrial pseudogenes: evolution’s misplaced witnesses [J]. Trends in Ecology and Evolution, 2001, 16(6):314-321.
[34] ZISCHLER H. Nuclear integrations of mitochondrial DNA in primates: inference of associated mutational events [J]. Electrophoresis, 2000, 21(3):531-536.
[35] VAUGHAN H E, HESLOPHARRISON J S, HEWITT G M. The localization of mitochondrial sequences to chromosomal DNA in orthopterans [J]. Genome, 1999, 42(5):874-880.
[36] SUNNUCKS P, HALES D F. Numerous transposed sequences of mitochondrial cytochrome oxidase Ⅰ-Ⅱ in aphids of the genus Sitobion (Hemiptera: Aphididae)[J]. Molecular Biology and Evolution, 1996, 13(3):510-524.
[37] KOUTROUMPA F A, LIEUTIER F, ROUX-MORABITO G. Incorporation of mitochondrial fragments in the nuclear genome (Numts) of the longhorned beetle Monochamus galloprovincialis (Coleoptera, Cerambycidae)[J]. Journal of Zoological Systematics and Evolutionary Research, 2009, 47(2):141-148.
[38] PALMER J D, ADAMS K L, CHO Y, et al. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates [J]. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(13):6960-6966.
[39] 陈志文, 王玉美, 聂虎帅, 等. 植物水平基因转移研究进展[J]. 中国农业大学学报, 2018, 23(1):1-11.
[40] SONG H, BUHAY J E, WHITING M F, et al. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified [J]. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(36):13486-13491.
[2] 张尚宏. 动物与植物线粒体基因组结构的差异—两种进化途径[J]. 动物学研究, 1995, 16(2):132-145.
[3] 黄族豪, 刘迺发. 动物线粒体基因组变异研究进展[J]. 生命科学研究, 2010, 14(2):166-171.
[4] BEAGLEY C T, OKIMOTO R, WOLSTENHOLME D R. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code [J].Genetics,1998,148(3):1091-1108.
[5] HELFENBEIN K G, FOURCADE H M, VANJANI R G, et al. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes [J]. Proceedings of the National Academy of Sciences of the United States of America,2004,101(29):10639-10643.
[6] MASTA S E, BOORE J L. Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes[J]. Molecular Biology and Evolution, 2008, 25(5):949-959.
[7] BECKENBACH A T, JOY J B.Evolution of the mitochondrial genomes of gall midges (Diptera: Cecidomyiidae): rearrangement and severe truncation of tRNA genes [J]. Genome Biology and Evolution, 2009, 1(1):278-287.
[8] SHAO Renfu, MITANI H, BARKER S C, et al. Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum [J]. Journal of Molecular Evolution, 2005, 60(6):764-773.
[9] SHAO Renfu, BARKER S C. The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes [J]. Molecular Biology and Evolution, 2003, 20(3):362-370.
[10] FUJITA M K, BOORE J L, MORITZ C. Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae)[J].Molecular Biology and Evolution,2007,24(12):2775-2786.
[11] LAVROV D V, BOORE J L, BROWN W M. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss[J].Molecular Biology and Evolution,2002,19(2):163-169.
[12] 邱忠营. 直翅目昆虫线粒体基因组比较、谱系及进化研究[D]. 西安:陕西师范大学, 2016.
[13] BURGER G, FORGET L, ZHU Yun, et al. Unique mitochondrial genome architecture in unicellular relatives of animals [J]. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100(3):892-897.
[14] SMITH D R, KAYAL E, YANAGIHARA A A, et al. First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution [J]. Genome Biology and Evolution, 2011, 4(1):52-58.
[15] SHAO Renfu, KIRKNESS E F, BARKER S C. The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus [J]. Genome Research, 2009, 19(5):904-912.
[16] LANG B F, LAFOREST M J, BURGER G. Mitochondrial introns: a critical view [J]. Trends in Genetics, 2007, 23(3):119-125.
[17] HAUSNER G. Fungal mitochondrial genomes, plasmids and introns [J]. Applied Mycology and Biotechnology,2003,3(3):101-131.
[18] BROWN G G, COLAS DES FRANCS-SMALL C, OSTERSETZER-BIRAN O. Group Ⅱ intron splicing factors in plant mitochondria [J]. Frontiers in Plant Science, 2014, 5(5):35.
[19] BEAGLEY C T, OKADA N A, WOLSTENHOLME D R. Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase [J]. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93(11):5619-5623.
[20] MEDINA M, COLLINS A G, TAKAOKA T L, et al. Naked corals: Skeleton loss in Scleractinia[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(24):9096-9100.
[21] TANG Sha, HYMAN B C. Mitochondrial genome haplotype hypervariation within the isopod parasitic nematode Thaumamermis cosgrovei [J].Genetics,2007,176(2):1139-1150.
[22] SNYDER M, FRASER A R, LAROCHE J, et al. Atypical mitochondrial DNA from the deep-sea scallop Placopecten magellanicus [J]. Proceedings of the National Academy of Sciences of the United States of America,1987,84(21):7595-7599.
[23] FULLER K M, ZOUROS E. Dispersed discrete length polymorphism of mitochondrial DNA in the scallop Placopecten magellanicus (Gmelin)[J]. Current Genetics, 1993, 23(4):365-369.
[24] SMITH D R, SNYDER M. Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome[J]. Journal of Molecular Evolution, 2007, 65(4):380-391.
[25] RIGAA A, MONNEROT M, SELLOS D. Molecular cloning and complete nucleotide sequence of the repeated unit and flanking gene of the scallop Pecten maximus mitochondrial DNA: putative replication origin features [J]. Journal of Molecular Evolution, 1995, 41(2):189-195.
[26] LIU Yunguo, KUROKAWA T, SEKINO M, et al. Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: an ultra-large metazoan mitochondrial genome [J]. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2012, 8(1):72-81.
[27] RAIMOND R, MARCADé I, BOUCHON D, et al. Organization of the large mitochondrial genome in the isopod Armadillidium vulgare [J]. Genetics, 1999, 151(1):203-210.
[28] BOYCE T M, ZWICK M E, AQUADRO C F. Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy[J]. Genetics, 1989, 123(4):825-836.
[29] YIN Jiao, HONG Guiyun, WANG Aiming, et al. Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other lepidopterans [J].Mitochondrial DNA Part A,2010,21(5):160-169.
[30] GRANT J R, STOTHARD P. The CGView Server: a comparative genomics tool for circular genomes [J]. Nucleic Acids Research, 2008, 36:w181-w184.
[31] HU Bo, JIN Jinpu, GUO Anyun, et al. GSDS 2.0: an upgraded gene feature visualization server [J].Bioinformatics, 2014, 31(8):1296-1297.
[32] KOHANY O, GENTLES A J, HANKUS L, et al. Annotation, submission and screening of repetitive elements in Repbase: Repbase Submitter and Censor [J]. BMC Bioinformatics, 2006, 7(1):474.
[33] HARTL D L. Mitochondrial pseudogenes: evolution’s misplaced witnesses [J]. Trends in Ecology and Evolution, 2001, 16(6):314-321.
[34] ZISCHLER H. Nuclear integrations of mitochondrial DNA in primates: inference of associated mutational events [J]. Electrophoresis, 2000, 21(3):531-536.
[35] VAUGHAN H E, HESLOPHARRISON J S, HEWITT G M. The localization of mitochondrial sequences to chromosomal DNA in orthopterans [J]. Genome, 1999, 42(5):874-880.
[36] SUNNUCKS P, HALES D F. Numerous transposed sequences of mitochondrial cytochrome oxidase Ⅰ-Ⅱ in aphids of the genus Sitobion (Hemiptera: Aphididae)[J]. Molecular Biology and Evolution, 1996, 13(3):510-524.
[37] KOUTROUMPA F A, LIEUTIER F, ROUX-MORABITO G. Incorporation of mitochondrial fragments in the nuclear genome (Numts) of the longhorned beetle Monochamus galloprovincialis (Coleoptera, Cerambycidae)[J]. Journal of Zoological Systematics and Evolutionary Research, 2009, 47(2):141-148.
[38] PALMER J D, ADAMS K L, CHO Y, et al. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates [J]. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(13):6960-6966.
[39] 陈志文, 王玉美, 聂虎帅, 等. 植物水平基因转移研究进展[J]. 中国农业大学学报, 2018, 23(1):1-11.
[40] SONG H, BUHAY J E, WHITING M F, et al. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified [J]. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(36):13486-13491.