背瘤丽蚌F型线粒体基因组全序列分析

Analysis on complete F type of mitochondrial genome in Lamprotula leai

部分双壳贝类的线粒体遗传方式是特殊的双重单亲遗传方式:F型存在于雌性体细胞组织和性腺中,M型仅存在于雄性个体的性腺中。通过LA-PCR扩增、SHOT-GUN测序、软件拼接获得背瘤丽蚌(Lamprotula leai)F型线粒体基因组全序列。线粒体基因组全长为16530 bp,包括13个蛋白质编码基因,22个tRNA其中包括2个tRNASer和2个tRNALeu,2个SrRNA及27个长度不等的非编码区,最长的两个非编码区分别为969 bp、228 bp。比较分析已登录到GenBank中的淡水蚌类F型线粒体结构特征,结果显示背瘤丽蚌F型A+T含量为60.28%,表现出A+T偏好性,淡水蚌类线粒体基因组长度的差异主要表现为非编码区长度的差异。此外,背瘤丽蚌mtDNA的COⅡ-12S rRNA区域基因排列存在差异,是ND3、tRNAHis、tRNAAla、tRNASer1、tRNASer2、tRNAGlu、ND2、tRNAMet8个基因发生重排造成。F型线粒体序列构建的系统进化树中,淡水蚌类和海水双壳贝类分别聚为一支。研究结果为进一步研究淡水珍珠蚌的DUI线粒体遗传方式和种质资源保护奠定基础,为双壳贝类mtDNA基因重排提供依据。

Lamprotula leai is an important freshwater mussel for pearl production.Doubly Uniparental Inheritance（DUI） is one of the most striking exceptions to the general rule of strict maternal transmission of mitochondrial DNA（mtDNA） in animals,and characterized by the presence of gender-associated mtDNA lineages that are inherited through male（male-transmitted or M type） or female（female-transmitted or F type） respectively.The complete mitochondrial genome of F type of Lamprotula leai was obtained using long and accurate polymerase chain reaction（LA-PCR）,shotgun sequencing.The genome contains 16,530 base pairs and 13 protein-coding genes,22 transfer RNA genes including 2 tRNASer and 2 tRNALeu,anticodons are tRNALeu1（UUR）=（TAA）,tRNALeu2（CUN）=（TAG）,tRNASer1（AGN）=（TCT）,tRNASer2（UCN）=（TGA）,2 ribosomal RNA genes,and 27 non-coding regions.The base composition for is 36.34%A,23.94%T,27.17% C,12.55%G and 60.28%（A＋T）.Most genes are encoded on the L strand while ND3—ND5,ND4L,COⅠ—COⅢ,ATP8,ATP6,tRNAAsp,tRNAHis are encoded on the H strand.The structure and organization of mitochondrial genomes of L.leai and other six freshwater mussels were analyzed using comparative genomics and bioinformatics methods.Results showed that：（ⅰ） Strong bias is toward A＋T for the F type genome of L.leai.（ⅱ） The striking mitochondrial genome difference in the size performed on the non-coding regions in all these freshwater mussels.（ⅲ） The gene arrangement of L.leai is identical to that of Hyriopsis cumingii,but is different from that of Cristaria plicata,Lampsilis ornate,Pyganodon grandis,Quadrula quadrulaand and Venustaconcha ellipsiformis between COⅡ and 12S rRNA.Therefore,the F type of freshwater mussels exist two gene orders between COⅡ and 12S rRNA： one is COⅡ-ND3-H-A-S1-S2-E-ND2-M-W-R-rrnS,another is COⅡ-H-S1-ND2-M-ND3-A-S2-E-W-R-rrnS.The difference is caused by rearrangement of 8 genes,including ND3,tRNAHis,tRNAAla,tRNASer1,tRNASer2,tRNAGlu,ND2 and tRNAMet.（ⅳ） 13 protein genes contain 4 initiation codons which are I（AUU,AUC）,V（GUG）,M（AUA）,L（UUG） and the stop codons of UAA or UAG with the exception of ND4 with incomplete T.（ⅴ） Analysis show that most of 22 tRNAs have typical cloverleaf structures,the acceptor of tRNALys and tRNAThr have bulge loop for T and A base unpairing,the anticodon loop of tRNAS2 has 9 bases.5 kinds of base unpairing are showed in the secondary structure of tRNA,such as A-C,A-A,G-T,T-T and T-C,in acceptor,D-loop and TψC loop.（ⅵ） 27 noncoding regions exist in L.leai,ranging in size from 1 to 969 bp.4 largest noncoding regions are found between ND5-tRNAGln（969bp）,tRNAGlu-tRNATrp（288 bp）,ND3-tRNATrp（116 bp）,and tRNAHis-tRNASer（114 bp）,only the 116 bp noncoding regions has an high A＋T content（A＋T=74.14%）.（ⅶ） Phylogenetic trees show that L.leai is clustered together with other freshwater mussels and far away from marine bivalves.The results of this study provide basic information for genetic resources and rule of DUI transmission of mtDNA in freshwater mussel,also provide the basis and model for gene rearrangement of mitochondrial genome in bivalves.