Bird Mitochondrial Gene Order: Insight from 3 Warbler Mitochondrial Genomes

Abstract

Two main gene orders exist in birds: the ancestral gene order and the remnant control region (CR) 2 gene order. These gene orders differ by the presence of 1 or 2 copies of the CR, respectively. Among songbirds, Oscines were thought to follow the ancestral gene order, with the exception of the lyrebird and Phylloscopus warblers. Here, we determined the complete mitochondrial genome sequence of 3 non-Phylloscopus warblers species and found that the blackcap (Sylvia atricapilla) and the reed warbler (Acrocephalus scirpaceus) have 2 almost identical copies of the CR, whereas the eastern orphean warbler (Sylvia crassirostris) follows the remnant CR 2 gene order. Our results contradict previous studies suggesting that Acrocephalus and most sylvioid warblers exhibit the ancestral gene order. We were able to trace this contradiction to a misidentification of gene order from polymerase chain reaction length determination. We thus suggest that passerine gene order evolution needs to be revised.

A novel mitochondrial gene order in shorebirds (Scolopacidae, Charadriiformes)

“…Since then gene duplications and re-arrangements have arisen independently several times among birds (Gibb et al, 2007;Haring et al, 1999;Mindell et al, 1998;Singh et al, 2008). They occur more often around the CR, a site for initiation and termination of DNA replication, than elsewhere in the mitochondrial genome (Fujita et al, 2007).…”

“…Sequence variation in the highly polymorphic CR and variations in gene order have both been applied as markers in phylogeographic and population genetic studies (Avise, 2000;Bensch and Härlid, 2000;Gibb et al, 2007;Mindell et al, 1998;Singh et al, 2008). However, gene duplications and re-arrangements complicate the usage of the CR as a marker.…”

“…In vertebrates, evidence for concerted evolution of duplicate CR regions has been found in fish (Tatarenkov and Avise, 2007), frogs (Kurabayashi et al, 2008), snakes (Jiang et al, 2007), and birds (parrots (Eberhard et al, 2001), albatrosses (Abbott et al, 2005) and warblers (Singh et al, 2008)). We discuss two alternative explanations for the high similarity of the two CRs in ruffs: (1) recent duplication of the CR with enough time for fixation but not enough to accumulate mutations, or (2) concerted evolution (Tatarenkov and Avise, 2007).…”

The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes)

“…Duplicate CRs have been detected in various birds, such as warblers (Sylvia atricapilla and Acrocephalus scirpaceus) (Singh et al, 2008), the blackfaced spoonbill (Platalea minor) (Cho et al, 2009), various seabird species (Sula leucogaster, Sula sula, and Sula nebouxii) (Morris-Pocock et al, 2010), and the parrot genus Amozona (Eberhard et al, 2001). In Charadriiformes, a duplicate CR with a high degree of similarity has been reported to exist in the mtDNA of a Scolopacidae species, the ruff Philomachus pugnax (Verkuil et al, 2010).…”

Complete mitochondrial genome of the Chinese Hwamei Garrulax canorus (Aves: Passeriformes): the first representative of the Leiothrichidae family with a duplicated control region

“…In G. canorus, the CR1 and CR2 sequences were identical for over 1000 bp (only the first ~70 bp of both CRs and the last ~90 bp of CR2 were not identical). The high level of similarity of CR1 and CR2 sequences suggests either a recent and independent duplication of the CR or concerted evolution (Singh et al, 2008). In comparison with CR1, CR2 has bidirectional LSP/HSP-like promoters, a sequence similar to the mammalian LSP/HSP (light-and heavy-strand transcription promoters) (Randi and Lucchini, 1998) (Figure 3).…”