Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis -a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea ?

• Published in: BMC Genomics
• Main Authors: Kong Xiaoyu, Wei Zhengpeng, Yu Ziniu, Shi Wei
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2008
• Subjects: Biotechnology; TP248.13-248.65; Genetics; QH426-470; Crassostrea gigas
• Online Access: https://doi.org/10.1186/1471-2164-9-477; https://doaj.org/article/af00833435a0435e943814e484b99105

Abstract Background Mitochondrial DNA sequences are extensively used as genetic markers not only for studies of population or ecological genetics, but also for phylogenetic and evolutionary analyses. Complete mt-sequences can reveal information about gene order and its variation, as well as gene and genome evolution when sequences from multiple phyla are compared. Mitochondrial gene order is highly variable among mollusks, with bivalves exhibiting the most variability. Of the 41 complete mt genomes sequenced so far, 12 are from bivalves. We determined, in the current study, the complete mitochondrial DNA sequence of Crassostrea hongkongensis . We present here an analysis of features of its gene content and genome organization in comparison with two other Crassostrea species to assess the variation within bivalves and among main groups of mollusks. Results The complete mitochondrial genome of C. hongkongensis was determined using long PCR and a primer walking sequencing strategy with genus-specific primers. The genome is 16,475 bp in length and contains 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 22 transfer tRNA genes (including a suppressor tRNA gene), and 2 ribosomal RNA genes, all of which appear to be transcribed from the same strand. A striking finding of this study is that a DNA segment containing four tRNA genes ( trnk1, trnC, trnQ1 and trnN ) and two duplicated or split rRNA gene ( rrnL5' and rrnS ) are absent from the genome, when compared with that of two other extant Crassostrea species, which is very likely a consequence of loss of a single genomic region present in ancestor of C. hongkongensis . It indicates this region seem to be a "hot spot" of genomic rearrangements over the Crassostrea mt-genomes. The arrangement of protein-coding genes in C. hongkongensis is identical to that of Crassostrea gigas and Crassostrea virginica , but higher amino acid sequence identities are shared between C. hongkongensis and C. gigas than between other pairs. There exists significant ...