Gene duplication and concerted evolution of mitochondrial DNA in crane species

Akiyama, Takuya; Nishida, Chizuko; Momose, Kunikazu; Onuma, Manabu; Takami, Kazutoshi; Masuda, Ryuichi

doi:10.1016/j.ympev.2016.09.026

Cited by 25 publications

(56 citation statements)

References 36 publications

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“…Taking into account the heterogeneity of the obtained DNA fragments as well as the fact that most of the tested reactions failed, we can conclude that the PCR products presented in Figure S4 in Additional le 1 were not ampli ed on the mitochondrial genome template. The D-F and D-R primers as well as the applied PCR are highly speci city and diagnostic for the presence of control region duplication in parrots [23], cranes [12] as well as blackbrowed albatross, ivory-billed aracari and osprey [4]. Therefore, the seven positive amplicons most likely represent mitochondrial DNA fragments located in the nuclear genomes, i.e.…”

Section: Duplicated Gene Order Identi Ed In Mitogenomes Of Analysed Pmentioning

confidence: 99%

“…Accordingly, recent analyses of additional parrot mitogenomes showed that the last common ancestor of Psittaciformes had a duplicated control region with adjacent genes [23]. The same could be true for Accipitriformes [4,5,[36][37][38], Falconiformes [4,39], Gruidae [12] and Pelecaniformes [4,15,16] because all or almost all members of these groups contain mitogenomes with the duplicated regions.…”

Section: Introductionmentioning

confidence: 99%

“…However, the growing number of avian mitochondrial genomes sequenced in recent years has revealed that other gene orders may be also be present in a frequency higher than it was previously thought. To date, several distinct variations of mitochondrial rearrangements have been reported in many representatives of the following avian orders: Accipitriformes [4,5], Bucerotiformes [6], Charadriiformes [7], Coraciiformes [8], Cuculiformes [9][10][11], Falconiformes [4], Gruiformes [12], Passeriformes [13,14], Pelecaniformes [4,15,16], Phoenicopteriformes [17,18], Piciformes [4,19], Procellariiformes [20,21], Psittaciformes [22,23], Strigiformes [24], Suliformes [15,20,25] and Tinamiformes [26]. All these rearrangements include an additional region between ND5 and tRNA-Phe genes, which seems to be particularly susceptible to duplication.…”

Section: Introductionmentioning

confidence: 99%

“…The most fully duplicated avian region (GO-FD; Fig. 1) was found in mitogenomes of all representatives of Gruidae [12] and Suliformes [15,20,25,27], the majority of Pelecaniformes [4,16] and Procellariiformes [4,21,28], as well as some Bucerotiformes and Psittaciformes species [6,23]. All other avian gene orders containing the duplicated elements result from subsequent degenerations of the rearrangement GO-FD due to pseudogenization or loss of some genes and/or control region [22,23].…”

Section: Introductionmentioning

confidence: 99%

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New View on the Organization and Evolution of Palaeognathae Mitogenomes Poses The Question on the Ancestral Gene Rearrangement in Aves

Urantówka

Kroczak

Mackiewicz

2020

Preprint

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BackgroundBird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, first identified in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily omitted due to inappropriate DNA amplification or genome sequencing, and may thus be readily overlooked. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds (Neognathae). So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. ResultsTherefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moa. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Included data for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves may also possess the mitogenomic duplication.ConclusionsThe duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assesses the potential selective advantages of the mitogenome duplications.

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Section: Duplicated Gene Order Identi Ed In Mitogenomes Of Analysed Pmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

New View on the Organization and Evolution of Palaeognathae Mitogenomes Poses The Question on the Ancestral Gene Rearrangement in Aves

Urantówka

Kroczak

Mackiewicz

2020

Preprint

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show abstract

“…Mitochondrial DNA. Where DNA quality allowed, we also sequenced large parts of copy 2 of the mitochondrial control region [38] using primers L16707 and H1247 [39] spanning a fragment of c. 1000 bp in A. antigone and 1150 bp in three specimens of A. rubicunda; one from the Gulf plains and two from the Atherton Tablelands (see [19]), which we used as outgroup in the phylogenetic analyses. In some specimens we had to target a shorter fragment using the forward primer L514 instead resulting in lengths of c.610 bp.…”

Section: Plos Onementioning

confidence: 99%

Subspecies in the Sarus Crane Antigone antigone revisited; with particular reference to the Australian population

et al. 2020

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Subspecies are often less well-defined than species but have become one of the basic units for legal protection. Evidence for the erection or synonymy of subspecies therefore needs to be founded on the best science available. Here we show that there is clear genetic disjunction in the Sarus Crane Antigone antigone, where previously the variation had appeared to be clinal. Based on a total sample of 76 individuals, analysis of 10 microsatellite loci from 67 samples and 49 sequences from the mitochondrial control region, this research establishes that the Australian Sarus Crane A. a. gillae differs significantly from both A. a. antigone (South Asia) and A. a. sharpii (Myanmar and Indochina). A single sample from the extinct Philippine subspecies A. a luzonica clustered with A. a. gillae, hinting at the potential for a more recent separation between them than from A. a. antigone and A. a. sharpii, even though A. a. sharpii is closer geographically. The results demonstrate that failure to detect subspecies through initial genetic profiling does not mean discontinuities are absent and has significance for other cases where subspecies are dismissed based on partial genetic evidence. It could also be potentially important for sourcing birds for reintroduction to the Philippines.

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Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta)

Meng,

Wang,

Pang

et al. 2024

Arch Insect Biochem Physiol

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The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age‐related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple‐CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.

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Gene duplication and concerted evolution of mitochondrial DNA in crane species

Cited by 25 publications

References 36 publications

New View on the Organization and Evolution of Palaeognathae Mitogenomes Poses The Question on the Ancestral Gene Rearrangement in Aves

New View on the Organization and Evolution of Palaeognathae Mitogenomes Poses The Question on the Ancestral Gene Rearrangement in Aves

Subspecies in the Sarus Crane Antigone antigone revisited; with particular reference to the Australian population

Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta)

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