The mitogenomes of <i>Gelochelidon nilotica</i> and <i>Sterna hirundo</i> (Charadriiformes, Sternidae) and their phylogenetic implications

Yang, Chao; Wang, Qingxiong; Li, Xuejuan; Yuan, Hao; Xiao, Hong; Huang, Yuan

doi:10.1080/23802359.2017.1372709

Cited by 6 publications

(4 citation statements)

References 15 publications

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“…2c). In the case of the common tern (Sterna hirundo), the current RefSeq sequence (PCR and Sanger sequencing [46]) was missing a duplication in the CR involving the MT-CYB, MT-TT, MT-TL2, MT-ND6, and MT-TE genes, as well as a substantial fraction of a tandem repeat. In the case of the Indo-Pacific tarpon (Megalops cyprinoides), a~650-bp tandem repeat was represented in the RefSeq reference (long-range PCR and direct Sanger sequencing [47]) for two thirds of its length, and the sequence downstream was completely absent, for~500 bp.…”

Section: Novel Duplications Repeats and Heteroplasmymentioning

confidence: 99%

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

et al. 2021

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Background Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

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Section: Novel Duplications Repeats and Heteroplasmymentioning

confidence: 99%

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

et al. 2021

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“…DNA was extracted using DNeasy Blood and Tissue kit (Quiagen, Hilden Germany) following the manufacturer's protocol. To amplify ~800 bp long fragment of the control region, we designed primers SH-mtCR4F (AACACCCATC-CAACTCGGAA) and SH-mtCR4R (AAT-TTCACTGTCGTTGACGTGT) using the mitogenome sequence from GeneBank (Yang et al 2017). PCR conditions were as follows: 3 min denaturation at 95°C, followed by 40 cycles of 30s at 95°C, 45s of annealing at 52°C, and 45s of elongation at 72°C.…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial DNA control region diversity in Common Terns Sterna hirundo from Slovenia and Croatia

et al. 2019

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Abstract63 Common Tern Sterna hirundo samples from Croatia and Slovenia were analysed with respect to their genetic diversity and differentiation. Samples originated from two freshwater populations (areas of the rivers Sava and Drava) and one coastal population (Sečovlje Salina). The molecular marker of choice was 709 bp long fragment of the mitochondrial control region, the fastest-evolving part of the mitochondrial genome. 21 haplotypes with 12 polymorphic sites were identified. Overall haplotype diversity was substantial and estimated at 0.8599, while the overall nucleotide diversity was low and estimated at 0.0025. Diversity indices were highest for the Drava population, followed by the Sava and the lowest for the Sečovlje population. Overall genetic structure was significantly low (Fst=0.0377) and attributed to the differences in haplotype frequencies between the populations. The high level of genetic diversity found in continental populations illustrates the importance of their habitats as reservoirs of genetic diversity and calls for their further protection and management.

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“…As of now, 47 complete mitochondrial genomes of Charadriiformes birds are available in the GenBank database. Among them, 13 mitogenomes of 11 Laridae species were generated from different geographical regions (Slack et al 2007;Ryu and Hwang 2012;Yang et al 2012Yang et al , 2016Yang et al , 2017Yoon et al 2015;Dong et al 2016;Kim and Park 2016;Anmarkrud and Lifjeld 2017;Skujina et al 2019). The analysis of the complete mitogenomes was also evidenced to characterize various genomic traits within protein-coding genes (PCGs), ribosomal RNA (rRNA), transfer RNA (tRNA), and control region (CR) as well as to detect gene order evolution in birds (Bensch and H€ arlid 2000;Crochet and Desmarais 2000;Ruokonen and Kvist 2002;Pacheco et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genome ofChroicocephalus brunnicephalusfrom India: phylogeny with other Larids

Kundu

Tyagi

Alam

et al. 2021

Mitochondrial DNA Part B

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The complete mitogenome sequence of the brown-headed gull, Chroicocephalus brunnicephalus was determined in this study. The 16,771 bp genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The decoded mitogenome was AT-rich (54.77%) with nine overlapping and 17 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. Further, the usual termination codons (AGG, TAG, TAA, and AGA) were used by 11 PCGs except for cox3 and nad4. The concatenated PCGs based Bayesian phylogeny clearly discriminates all the Laridae species and reflects the sister relationship of C. brunnicephalus with C. ridibundus. The present mitogenome-based phylogeny was congruent with the earlier hypothesis and confirmed the evolutionary position of the brownheaded gull as masked species. The generated mitogenome of C. brunnicephalus is almost identical to the previously generated mitogenome from China except for two base pairs in CR. To visualize the population structure of this migratory species, we propose more sampling from different geographical locations and the generation of additional molecular data to clarify the reality.

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The mitogenomes of Gelochelidon nilotica and Sterna hirundo (Charadriiformes, Sternidae) and their phylogenetic implications

Cited by 6 publications

References 15 publications

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Mitochondrial DNA control region diversity in Common Terns Sterna hirundo from Slovenia and Croatia

Complete mitochondrial genome ofChroicocephalus brunnicephalusfrom India: phylogeny with other Larids

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