Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets
© Yu et al; licensee BioMed Central Ltd. 2009
Received: 26 January 2009
Accepted: 05 May 2009
Published: 05 May 2009
It can be seen from the available mollusk mitogenomes that the family Pectinidae exhibits the most variation in genome organization. In this study, comparative mitogenomic analyses were performed for three scallops from the subfamily Chlamydinae (Pectinidae), with the goal of characterizing the degree of variability of mitogenome organization and other characteristics among species from the same subfamily and exploring their possible evolution route.
The complete or nearly complete mtDNA sequences of scallop Mimachlamys nobilis (17 935 bp), Mizuhopecten yessoensis (20 964 bp) and Chlamys farreri (17 035 bp) were determined using long PCR amplification and primer walking sequencing strategy. Highly variable size difference of the three genomes resulted primarily from length and number variations of non-coding regions, and the major difference in gene content of the three scallop species are due to varying tRNA gene sets. Only 21, 16, and 17 tRNA genes were detected in the mitogenomes of M. nobilis, M. yessoensis and C. farreri, respectively. Remarkably, no trnS gene could be identified in any of the three scallops. A newly-detected trnA-like sequence within the mitogenome of M. yessoensis seems to exemplify the functional loss of a tRNA gene, and the duplication of trnD in M. yessoensis raises a fundamental question of whether the retention of the tRNA gene copy of 2-tRNAs is easier than that of 4-tRNAs. Analysis of putative evolutionary pathways of gene rearrangement indicates that transposition of neighboring gene blocks may play an important role in the evolution of mitogenomes in scallops. Parsimonious analysis of the genomic variations implies that the mitogenomes of M. yessoensis and C. farreri are likely to derive independently from a common ancestor that was closely related to M. nobilis.
Comparative mitogenomic analyses among three species from the subfamily Chlamydinae show that the three genomes exhibit a high level of genomic variation and a diversity of tRNA gene sets, characterized by extensive translocation of genes. These features provide useful clues and information for evolutionary analysis of scallop mitogenomes.
It can be seen from the available mollusk mitogenomes that the Pectinidae exhibits the most variation in genome organization. When we were initiating the current study, three complete or nearly complete mitogenomes, representing three subfamilies, were available from this family, i.e., Argopecten irradians (Aequipectini group, GenBank: EU023915), Mizuhopecten yessoensis (Chlamydinae, GenBank: AB271769) and Placopecten magellanicus (Palliolinae, GenBank: DQ088274). Obvious differences in mitogenome organization of three scallops were observed: 1) the sizes of three mitogenomes are distinct from each other, i.e. 16 221 bp for A. irradians, 20 414 bp for M. yessoensis and 32 115 bp for P. magellanicus ; 2) allegedly, the three mitogenomes have significantly different tRNA gene sets, with the numbers of 22, 32 and 9 for A. irradians, P. magellanicus and M. yessoensis, respectively; 3) the genomes show distinct gene arrangement patterns, namely unique rearrangements involving nearly every gene.
The degree of gene arrangements of mitogenomes from different species in the same subfamily, Chlamydinae, is one of our concerns. Therefore, in this study the complete mtDNA sequences of Mimachlamys nobilis and M. yessoensis, and nearly complete mtDNA sequence of Chlamys farreri are determined using long PCR amplification and primer walking sequencing strategy (see Additional file 1), and used for comparative analyses. Another reason for inclusion of M. yessoensis is that its first mitogenome data deposited in GenBank (AB271769) seems to bear significant omissions and mis-annotations of tRNA genes and protein-coding gene. Apparently, these mis-annotations need to be amended for further studies of gene order variation, evolution and phylogenetic analysis.
Genome organization and nucleotide composition
The size of the mitogenome is 17 935 bp for M. nobilis (GenBank: FJ595958). Due to technical difficulties in sequencing, a small part (up to a couple of hundreds base pairs) of the mitogenome of C. farreri was not obtained and the nearly complete genome is 17 035 bp in length (GenBank: FJ595957). Genome assembly indicated that the unfinished section is the start part of the major non-coding region (MNR). The complete mtDNA sequence of M. yessoensis obtained in this study is 20 964 bp in length (GenBank: FJ595959), which is 550 bp longer than the nearly complete genome. Genome assembly indicated that the previously unfinished section is part of the MNR. Annotation to the mitogenome obtained in the current study and a re-annotation to AB271769 revealed the following findings: 1) the "absent" cox2 gene in previous annotation is actually present, corresponding to nucleotides 14 638–15 325, with "CTG" as initiation codon and "T" as termination codon; and 2) the genome has a total of 16 tRNA genes, instead of nine identified in that nearly complete genome. Additionally, 56 transitions were detected from a comparison of mitogenomes FJ595959 and AB271769.
Protein-coding gene assignments and identity of Mimachlamys nobilis (Mnob), Mizuhopecten yessoensis (Myes) and Chlamys farreri (Cfar)
In this study, most of PCGs in three mitogenomes use conventional initiation codons (20 for ATG, 10 for ATA and 1 for ATT), but two genes use the alternative ones (M. nobilis: nad1-TTG; M. yessoensis: cox2-CTG, nad1-GTG; C. farreri: cox2-GTG, nad1-GTG). Notably, one of the alternative initiation codons, GTG was also frequently used in two previously described scallop mitogenomes (5 for A. irradians and 2 for P. magellanicus). Only two genes use CTG as an initiation codon in the 45 reported molluscan mitogenomes (M. yessoensis: cox2; Lottia digitalis: cox1). Interestingly, six of 12 PCGs in M. yessoensis and C. farreri show a derived characteristic in their use of initiation codons when compared with those of M. nobilis, i.e. atp6 (ATA [M. nobilis]→ATG [M. yessoensis and C. farreri]), cox1 (ATA→ATG), cob (ATA→ATG), nad1 (TTG→GTG), nad2 (ATG→ATA) and nad4 (ATG→ATA). In general, the usage of initiation codons among three scallops is flexible, but not random.
Three genes stop with identical termination codon in all three scallops, i.e. nad1 (TAG), nad4 (TAG) and nad4L (TAA). Five genes (atp6, cox2, cox3, cob and nad2) share the same termination codon in the mitogenomes of C. farreri and M. nobili and three genes (cox1, nad3 and nad5) use the same termination codon in the genomes of M. yessoensis and M. nobilis. The nad6 in M. yessoensis and C. farreri display the derivative feature of termination codon usage when compared with that of M. nobilis (TAA [M. nobilis]→TAG [M. yessoensis and C. farreri]). The cox2 gene in both M. yessoensis and C. farreri contains a truncated termination codon, ending with a single thymine.
Transfer RNA genes
Despite an extensive search with the tRNAscan-SE  and by eye inspection, only 21, 16, and 17 tRNA genes were detected in the mitogenomes of M. nobilis, M. yessoensis and C. farreri, respectively (Additional file 7; Additional file 8; Additional file 9). Particularly, no trnS gene could be identified in any of the three scallops, and four tRNAs (trnG, trnV, trnW and trnY) were absent in the mitogenome of both M. yessoensis and C. farreri. Nevertheless, we presume that the loss of trnW and trnY in the mitogenome of C. farreri may be an artifact, due to unfinished sequencing of the region downstream of trnH. The loss of trnS may present the ancestral state for all three scallops of the subfamily Chlamydinae. The loss of the tRNA cluster "GV" in the mitogenome of M. yessoensis and C. farreri may present the first step of tRNA gene loss from the common ancestor of these two species belonging to the same tribe (Chlamydini). Additional derived features of tRNA gene loss and translocations were observed separately for both M. yessoensis and C. farreri, e.g. the deletions of trnH, trnW, trnY and trnA, and the duplication of trnD in the mitogenome of M. yessoensis.
In the mitogenomes of metazoan, almost all amino acids codons but leucine and serine are decoded by only one tRNA each . The presence of two trnM genes was reported in the mitogenomes of tunicates . However, it is a common phenomenon that mitogenomes of most bivalves contain two trnM genes. In this study, the trnM2 gene was found clustered with other tRNA genes, but the locations of trnM1 were variable over species. Another case of tRNA gene duplication is the trnD in M. yessoensis, which is found in single copy in the mitogenomes of both M. nobilis and C. farreri. Both trnD1 and trnD2 are considered true tRNA genes, based on sequence comparison (Figure 2B) as well as their putative secondary structures (Additional file 8). In order to probe into the mechanism of the retention of two copies of non-trnL/trnS tRNA genes, we examined the mitogenomes of all available mollusks for their tRNA gene usage, and found that a total of eight tRNA genes (trnD, trnE, trnF, trnK, trnM, trnN, trnQ, trnV) appear in at least two copies for each (see Additional file 10). Notably, all but trnV have anticodons corresponding to the 2-fold degenerate codons. This finding raises a fundamental question of whether the retention of the tRNA gene copy of 2-tRNAs is easier than that of 4-tRNAs (also see ). Perhaps there are differences in the gene loss and import mechanisms from the cytoplasm to the mitochondria of 4-tRNAs and 2-tRNAs. It is desirable to investigate the mechanisms of tRNA gene loss in further studies; more mitogenomes with variable tRNA gene sets should be included in future studies to draw a solid conclusion.
Putative evolutionary pathway of gene rearrangements
It has been commonly recognized that variations in gene order are relatively rare in mitogenomes of most metazoan lineages . Dowton et al.  estimated a probability of 1/2664 for a single event of gene translocation occurring independently in two mitogenomes (starting from the same gene order in both). However, this probability could be an underestimate according to yet unidentified constraints on modes of gene rearrangements, and it should be applied cautiously. Pectinid bivalves seem to represent another example, as five sequenced mitogenomes exhibit significant genomic rearrangements, suggesting that gene rearrangements occurred frequently among lineages in this family. On the other hand, high amino acid sequence identity between M. yessoensis and C. farreri indicate that these species may have diverged only recently. As illustrated in Figure 3, transposition of neighbor gene blocks (transposition 1, 3 and 4) may play an important role in the evolution of scallop mitogenomes. There is no doubt that mt genomic rearrangements are in most cases appropriate markers to resolve both ancient and recent divergence processes , but the result of this study implies that a careful estimation of the rearrangement pathway is especially required in analyzing the highly variable organizations of mitogenomes in the Pectinidae. However, the scallop mitogenomes with such diversity in their organization seem to be a good model to elucidate molecular evolutionary and phylogenetic issues of mitogenomes in future studies.
This work was financially supported by the CAS/SAFEA International Partnership Program for Creative Research Teams, Guangdong Science Foundation (No. 8451030101001660) and National Science Foundation of China (No. 40776088).
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