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A unique tRNA gene family and a novel, highly expressed ORF in the mitochondrial genome of the silver-lip pearl oyster, Pinctada maxima (Bivalvia: Pteriidae)
Wu, XY; Li, XL; Li, L; Yu, ZN; carlzyu@scsio.ac.cn
2012
Source PublicationGENE
ISSN0378-1119
Volume510Issue:1Pages:22-31
AbstractCharacteristics of mitochondrial (mt) DNA such as gene content and arrangement, as well as mt tRNA secondary structure, are frequently used in comparative genomic analyses because they provide valuable phylogenetic information. However, most analyses do not characterize the relationship of tRNA genes from the same mt genome and, in some cases, analyses overlook possible novel open reading frames (ORFs) when the 13 expected protein-coding genes are already annotated. In this study, we describe the sequence and characterization of the complete mt genome of the silver-lip pearl oyster, Pinctada maxima. The 16,994-bp mt genome contains the same 13 protein-coding genes (PCGs) and two ribosomal RNA genes typical of metazoans. The gene arrangement, however, is completely distinct from that of all other available bivalve mt genomes, and a unique tRNA gene family is observed in this genome. The unique tRNA gene family includes two trnS(-AGY) and trnQ genes, a trnM isomerism, but it lacks trnS(-CUN). We also report the first clear evidence of alloacceptor tRNA gene recruitment (trnP-->trnS(-AGY)) in mollusks. In addition, a novel ORF (orfUR1) expressed at high levels is present in the mt genome of this pearl oyster. This gene contains a conserved domain, "Oxidored_q1_N", which is a member of Complex I and thus may play an important role in key biological functions. Because orfUR1 has a very similar nucleotide composition and codon bias to that of other genes in this genome, we hypothesize that this gene may have been moved to the mt genome via gene transfer from the nuclear genome at an early stage of speciation of P. maxima, or it may have evolved as a result of gene duplication, followed by rapid sequence divergence. Lastly, a 319-bp region was identified as the possible control region (CR) even though it does not correspond to the longest non-coding region in the genome. Unlike other studies of mt genomes, this study compares the evolutionary patterns of all available bivalve mt tRNA and 148 genes. (C) 2012 Elsevier B.V. All rights reserved.
Department[Wu, Xiangyun; Li, Xiaoling; Li, Lu; Yu, Ziniu] Chinese Acad Sci, S China Sea Inst Oceanol, Guangdong Key Lab Appl Marine Biol, Key Lab Marine Bioresource Sustainable Utilizat, Guangzhou 510301, Guangdong, Peoples R China; [Li, Xiaoling] Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
KeywordPinctada Maxima Mitochondrial Genome Pearl Oyster Trna Gene Recruitment Atp8 Control Region
Subject AreaGenetics & Heredity
Language英语
Funding ProjectLMB
WOS IDWOS:000313611700004
Citation statistics
Document Type期刊论文
Identifierhttp://ir.scsio.ac.cn/handle/344004/9744
Collection中科院海洋生物资源可持续利用重点实验室
Corresponding Authorcarlzyu@scsio.ac.cn
Recommended Citation
GB/T 7714
Wu, XY,Li, XL,Li, L,et al. A unique tRNA gene family and a novel, highly expressed ORF in the mitochondrial genome of the silver-lip pearl oyster, Pinctada maxima (Bivalvia: Pteriidae)[J]. GENE,2012,510(1):22-31.
APA Wu, XY,Li, XL,Li, L,Yu, ZN,&carlzyu@scsio.ac.cn.(2012).A unique tRNA gene family and a novel, highly expressed ORF in the mitochondrial genome of the silver-lip pearl oyster, Pinctada maxima (Bivalvia: Pteriidae).GENE,510(1),22-31.
MLA Wu, XY,et al."A unique tRNA gene family and a novel, highly expressed ORF in the mitochondrial genome of the silver-lip pearl oyster, Pinctada maxima (Bivalvia: Pteriidae)".GENE 510.1(2012):22-31.
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