Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses)

Abstract

Although the tandem duplication of mitochondrial (mt) sequences, especially those of the control region (CR), has been detected in metazoan species, few studies have focused on the features of the duplicated sequence itself, such as the gene conversion rate, distribution patterns of the variation, and relative rates of evolution between the copies. To investigate the features of duplicated mt sequences, we partially sequenced the mt genome of 16 Phoebastria albatrosses belonging to three species (P. albatrus, P. nigripes, and P. immutabilis). More than 2,300 base pairs of tandemly-duplicated sequence were shared by all three species. The observed gene arrangement was shared in the three Phoebastria albatrosses and suggests that the duplication event occurred in the common ancestor of the three species. Most of the copies in each individual were identical or nearly identical, and were maintained through frequent gene conversions. By contrast, portions of CR domains I and III had different phylogenetic signals, suggesting that gene conversion had not occurred in those sections after the speciation of the three species. Several lines of data, including the heterogeneity of the rate of molecular evolution, nucleotide differences, and putative secondary structures, suggests that the two sequences in CR domain I are maintained through selection; however, additional studies into the mechanisms of gene conversion and mtDNA synthesis are required to confirm this hypothesis.

The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements

“…The tandem replication slippage sequentially homogenized sequences between duplications [19], therefore this mechanism cannot account for the observation in most ardeid species, where the homogenized duplications were interrupted by a divergent section nesting in the middle of CR domain I. In contrast, such uneven homogenized pattern could be easily created and maintained by gene conversion, similar to the previous reports in albatrosses [7, 12], the black-faced spoonbill [11], the ruff [13], boobies [14] and Philippine hornbills [15]. In albatrosses, Abbott et al [7] proposed that the gene conversion could have multiple recombination points, whereby certain duplicated portions were regularly homogenized while intervening sections remained unaffected and therefore evolved independently.…”

“…The duplicate tRNA Thr –CR gene order had previously been reported in Philippine hornbills [15], albatrosses [7, 12], the black-faced spoonbill [11], and several birds of “core” pelecaniforms [14]. The p-Cytb was significantly shorter in ardeid birds compared to these birds, which implies that the extant length of the p-Cytb in ardeid birds was not the initial duplicated piece, but resulted from degeneration of the 5’ end of p-Cytb.…”

“…However, in birds it is common that the duplications have persisted for a long evolutionary time, where both copies of the duplicated genes or CRs are functional and have high sequence similarity. Such situation has generally been thought to be due to concerted evolution and multiple mechanisms accounting for concerted evolution were postulated [5, 7, 8, 10, 12–15, 19, 20]. …”

“…Recent avian molecular phylogenies based on a large set of nuclear data [22] and complete mtDNA [17] have united the Ardeidae into a large taxonomic group that contains Pelecaniformes and Ciconiiformes. The duplicate tRNA Thr –CR gene order is taxonomically widespread within this group [7, 11, 12, 14, 17], suggesting that this mitochondrial gene order might be a general pattern in these related birds. However, the recently published complete mitochondrial DNA (mtDNA) sequences of four ardeid species indicate that their gene orders are similar to the ancestral gene order [8, 23, 24].…”

The Present Status of Available Genetic Information for Avian Species Distributing in Japan and on the List of “Nationally Endangered Species of Wild Fauna and Flora”

“…There are 82 mitochondrial DNA sequences: 46 control region sequences Kuro-o et al, 2010), 29 D-loop sequences (Eda et al, 2011(Eda et al, , 2012, three mitochondrial Cytochrome Oxidase Subunit I (COI) sequences (Saitoh et al, 2015) and four mitochondrial DNA sequences including Cytb-1, ND6-1, ND6-2 genes for Cytb, NADH dehydrogenase subunit 6, complete cds; Cytb-2 pseudogene for Cytb; tRNA-Thr-1, tRNA-Thr-2, tRNA-Pro-1, tRNA-Pro-2, tRNA-Glu-1, tRNAGlu-2, complete sequence; control region 1 complete sequence and control region 2 partial sequence . In addition, one DRD4 gene sequence (Abe et al, 2011) is registered.…”