文蛤线粒体基因组序列测定及进化分析
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摘要
文蛤(Meretrix meretrix)属软体动物门(Mollusca)、双壳纲(Lamellibranchia)、异齿亚纲(Heterodonta)、帘蛤目(Veneroida)、帘蛤科(Veneridae)、文蛤属(Meretrix)。文蛤是一种天然资源丰富的滩涂贝类,具有较高的营养和药用价值,是重要的海水增养殖优良品种,也是主要出口的鲜活水产品之一。本研究采用PCR扩增和基因克隆等常规分子生物学手段,并结合生物信息学方法对文蛤线粒体基因组全序列进行测定与分析。同时,探讨了双壳类线粒体基因的重排,采用NJ和MP法构建了双壳类的系统进化树。所获得的主要结论如下:
1.本研究所测定的文蛤线粒体基因组全序列长度为19,826bp,编码37个基因,包括2个rRNA基因、23个tRNA基因和12个蛋白质编码基因,所有的基因都由H链编码。与典型的后口动物相比,缺失了ATP8。
2.文蛤线粒体起始密码子包括ATG、ATA和TTG,终止密码子包括TAA和TAG。
3.文蛤mtDNA编码23个tRNA,长度在62 bp到71 bp之间,二级结构保守,全部能够折叠成典型的三叶草结构。缺少tRNA~(Ser(AGN)),但含有两个tRNA~(Gln)的拷贝,这在双壳类中是首次发现。
4.比较分析了双壳类线粒体基因的重排,在帘蛤科内,菲律宾蛤仔与文蛤和中华文蛤在基因排列上共享3个基因框:5’-COI-tRNA~(Leu(CUN))-ND1-ND2-ND4L- tRNA~(Ile)-3’,5’-COII-tRNA~(Pro)-Cyt b-16S rRNA-ND4- tRNA~(His)- tRNA~(Glu)-tRNA~(Ser(UCN))- ATP6-ND3-ND5-3’, and 5’- tRNA~(Asn)- tRNA~(Thr)-3’。。
5.应用ClustalX1.83和Mega4.0采用NJ法和MP法构建双壳纲系统进化树。所有物种分成4支,牡蛎科和扇贝科聚为一支;贻贝科和蚌科各自聚为一支;帘蛤科的三个物种聚为一支,置信度为100;然后和鸟蛤科聚为一支。
Hard clam (Meretrix meretrix) belongs to Mollusca, Lamellibranchia, Heterodonta, Veneroida, Veneridae, Meretrix, which is a natural resource-rich shellfish, and possess high nutritional and medical value. In this research, after amplifying mtDNA using Long-PCR and normal PCR methods, the complete mitochondrial genomes of Meretrix meretrix was determined and analyzed through directly sequencing PCR products or sequencing cloned PCR products. The organization and characteristic of the mitogenome, including gene order, base compositon, 13 protein coding genes, rRNA genes, 22tRNA genes, codon usage and amino-acid composition were surveyed. Finally, the rearrangement of mitochondrial genes in Bivalvia was analyzed and phylogenetic tree was constructed based on amino acid data. The conclusions drawn from the study as follows.
1. The entire mitochondrial (mt genome) sequence of M. meretrix is 19,826 bp in length, and contains 37 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 23 tRNAs. All genes are encoded on the heavy strand. In contrast to the typical animal mitochondrial genome, it lacks the protein-coding gene ATP8.
2. Mt genes commonly use several alternatives to ATG as start codons. Eight of twelve protein-coding genes (COII,COIII, ATP6, ND1, ND2, ND3, ND4, ND4L) of the clam initiate with ATG start codon, while Cyt b, ND5 and ND6 start with ATA and cox1 with TTG. Eight protein-coding genes use TAA as stop codon(COI, COII, ND2, ND3, ND4, ND4L, cob, atp6), and the remaining four genes terminate with TAG.
3. The clam mtDNA encodes 23 tRNA genes, ranging in size from 62(trnH) to 71(trnA) nucleotides. All 23 tRNAs have the typical clover-leaf structure. In contrast to the standard complement of 22 tRNA genes, the clam mt genome lacks tRN~(ASer(AGN)), and has two duplication of tRNA~(Gln), that is the first report in Bivalvia.
4. Comparing the gene arrangement among M. meretrix, M. petechialis and Venerupis philippinarum, we observed that the gene arrangement between M. petechialis and M. meretrix are the same except for one more tRNA~(Gln) gene in M. meretrix mt genome than in M. petechialis and the gene arrangement between two species of the genus Meretrix and V. philippinarum share three completely large identical gene blocks. 5. Phylogenetic analyses based on amino acid data show that twenty three bivalve species are divided into 4 clades. The M. meretrix is placed in a clade containing of Veneridae, Solenidae, Cardiidae and Saxicavidae, which places the grouping composed with Ostridae and Pectinidae as the sister groups.
1.本研究所测定的文蛤线粒体基因组全序列长度为19,826bp,编码37个基因,包括2个rRNA基因、23个tRNA基因和12个蛋白质编码基因,所有的基因都由H链编码。与典型的后口动物相比,缺失了ATP8。
2.文蛤线粒体起始密码子包括ATG、ATA和TTG,终止密码子包括TAA和TAG。
3.文蛤mtDNA编码23个tRNA,长度在62 bp到71 bp之间,二级结构保守,全部能够折叠成典型的三叶草结构。缺少tRNA~(Ser(AGN)),但含有两个tRNA~(Gln)的拷贝,这在双壳类中是首次发现。
4.比较分析了双壳类线粒体基因的重排,在帘蛤科内,菲律宾蛤仔与文蛤和中华文蛤在基因排列上共享3个基因框:5’-COI-tRNA~(Leu(CUN))-ND1-ND2-ND4L- tRNA~(Ile)-3’,5’-COII-tRNA~(Pro)-Cyt b-16S rRNA-ND4- tRNA~(His)- tRNA~(Glu)-tRNA~(Ser(UCN))- ATP6-ND3-ND5-3’, and 5’- tRNA~(Asn)- tRNA~(Thr)-3’。。
5.应用ClustalX1.83和Mega4.0采用NJ法和MP法构建双壳纲系统进化树。所有物种分成4支,牡蛎科和扇贝科聚为一支;贻贝科和蚌科各自聚为一支;帘蛤科的三个物种聚为一支,置信度为100;然后和鸟蛤科聚为一支。
Hard clam (Meretrix meretrix) belongs to Mollusca, Lamellibranchia, Heterodonta, Veneroida, Veneridae, Meretrix, which is a natural resource-rich shellfish, and possess high nutritional and medical value. In this research, after amplifying mtDNA using Long-PCR and normal PCR methods, the complete mitochondrial genomes of Meretrix meretrix was determined and analyzed through directly sequencing PCR products or sequencing cloned PCR products. The organization and characteristic of the mitogenome, including gene order, base compositon, 13 protein coding genes, rRNA genes, 22tRNA genes, codon usage and amino-acid composition were surveyed. Finally, the rearrangement of mitochondrial genes in Bivalvia was analyzed and phylogenetic tree was constructed based on amino acid data. The conclusions drawn from the study as follows.
1. The entire mitochondrial (mt genome) sequence of M. meretrix is 19,826 bp in length, and contains 37 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 23 tRNAs. All genes are encoded on the heavy strand. In contrast to the typical animal mitochondrial genome, it lacks the protein-coding gene ATP8.
2. Mt genes commonly use several alternatives to ATG as start codons. Eight of twelve protein-coding genes (COII,COIII, ATP6, ND1, ND2, ND3, ND4, ND4L) of the clam initiate with ATG start codon, while Cyt b, ND5 and ND6 start with ATA and cox1 with TTG. Eight protein-coding genes use TAA as stop codon(COI, COII, ND2, ND3, ND4, ND4L, cob, atp6), and the remaining four genes terminate with TAG.
3. The clam mtDNA encodes 23 tRNA genes, ranging in size from 62(trnH) to 71(trnA) nucleotides. All 23 tRNAs have the typical clover-leaf structure. In contrast to the standard complement of 22 tRNA genes, the clam mt genome lacks tRN~(ASer(AGN)), and has two duplication of tRNA~(Gln), that is the first report in Bivalvia.
4. Comparing the gene arrangement among M. meretrix, M. petechialis and Venerupis philippinarum, we observed that the gene arrangement between M. petechialis and M. meretrix are the same except for one more tRNA~(Gln) gene in M. meretrix mt genome than in M. petechialis and the gene arrangement between two species of the genus Meretrix and V. philippinarum share three completely large identical gene blocks. 5. Phylogenetic analyses based on amino acid data show that twenty three bivalve species are divided into 4 clades. The M. meretrix is placed in a clade containing of Veneridae, Solenidae, Cardiidae and Saxicavidae, which places the grouping composed with Ostridae and Pectinidae as the sister groups.
引文
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[3] Nass MMK, Nass S. Intramitochondrial fibers with DNA characteristics[J]. J Cell Biol, 1963, 19: 593-611.
[4]牛屹东,李明,魏辅文,等.线粒体DNA用作分子标记的可靠性和研究前景.遗传, 2001, 23(6): 593-598.
[5] Bridge D, Cunningham CW and Schierwater B. Class-lever relationships in the phylum Cnidaria, evidence from mitochondrial genome structure[J]. Proc Natl Acad Sci. USA, 1992, 89: 8750-8753.
[6] Ojala D, Montoya J and Attardi G. tRNA punctuation model of RNA processiong in human mitochondria[J]. Nature, 1981, 290: 470-474.
[7]陈复生,付承玉,汪泰初.动物线粒体基因分子系统学研究进展[J].安徽农业科学, 2003, 31(4):596-598.
[8]廖顺尧,鲁成.动物线粒体基因组研究进展[J].生物化学与生物物理进展, 2000, 27(5): 509-512.
[9] Boore JL, Brown WM. Complete DNA Sequence of the Mitochondrial Genome of the Black Chiton,Katharina tunicata[J]. Genetics, 1994, 138:423–443.
[10] Beagley CT, Macfarlane JL, Pont KA. Mitonchondrial genomes of Anthozoa(Cnidaria)[J]. Peogress in Cell Research, 1995, 5:149-153.
[11] Ren J, Shen X, Sun M, Jiang F, Yu Y, Chi Z Liu B. The complete mitochondrial genome of the clam Meretrix petechialis (Mollusca: Bivalvia: Veneridae). Mitochondrial DNA, 2009, 20:78–87.
[12] Crozier RH, Crozier YC. The mitochondrial genome of the honeybee apis mellifera: complete sequence and genome organization[J]. Genetics, 1993, 133(1): 97-117
[13] Boore JL, Brown WM. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicate[J]. Genetics, 1994, 138(2): 423-443.
[14] Beagley CT, Macfarlane JL, Pont KA. Mitochondrial genomes of Anthozoa(Cnidaria)[J]. Progress in Cell Research, 1995, 5: 149-153.
[15] Breton S, Burger G, Stewart DT, Blier PU. Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels(Mytilus spp.). Genetics, 2006, 172: 1107-1119.
[16] Yu ZN, Wei ZP, Kong XY, Shi W. Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of“Tandem duplication-random loss”for genome rearrangement in Crassostrea[J]. BMC Genomics, 2008, 9: 477.
[17] Orti G, Petry P, Porto JIR. Patterns of nucleotide change in mitochondrial ribosomal RNA genes and the phylogeny of piranhas[J]. Journal of Molecular Evolution, 1996, 42(2): 169-182.
[18] Tartar AL, Boucias DG, Becnel JJ. Comparison of plastid 16S rRNA genes from Helicosporidium spp.: evidence supporting the reclassification of Helicosporidia as green algae (Chlorophyta)[J]. International Journal of Systematic and Evolutionary Microbiology, 2003, 53: 1719-1723.
[19]李爱玲,张志芳,潘沈元.昆虫线粒体DNA A+T富集区的研究及其在分子进化中的应用[J].中国蚕业, 2004, 25(1): 70-72.
[20] Southern SO, Southern PJ, Dizon AE. Molecular characterization of a cloned dolphin mitochondrial genome[J]. J Mol Evol, 1989,28(2): 32-42.
[21] Sbisa E, Tanzariello G, Reyes A, et al. Mammalian mitochondrial D-loopregion structural analysis: Identification of new conserved sequence and their functional and evolutionary implications[J]. Gene, 1997, 205(1-2): 125-140.
[22]黄原.分子系统学-原理方法及应用[M].北京:中国农业出版社, 1998.
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