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Thursday, 30 January 2014

Mitochondrial DNA sequence research in birds; helping to understand evolution and speciation.

Mitochondria are the power-stations of the cell, producing an energy supply for the various cellular processes. To ensure this demand never fails, these organelles have their own DNA that is separate from the majority of the cell's DNA that is kept in the nucleus. This mtDNA has a relatively short sequence and codes for only a few genes. The 16,775 base-pair mitochondrial genome of the white Leghorn chicken has been cloned and sequenced, and has a set of 37 genes for 13 proteins, 2 ribosomal RNAs and 22 transfer RNAs. Mitochondrial DNA sequencing can be used as a type of 'genetic barcoding' that allows for examination of evolution and species definition. An example of such work can be seen in the following paper on Black-Tailed Godwits.

Patterns in Nuclear and Mitochondrial DNA Reveal Historical and Recent Isolation in the Black-Tailed Godwit (Limosa limosa)


Krijn B. Trimbos, Camiel Doorenweerd, Ken Kraaijeveld, C. J. M. Musters, Niko M. Groen, Peter de Knijff, Theunis Piersma, and Geert R. de Snoo
PLoS One. 2014; 9(1): e83949.
Published online 2014 January 9.
LINK

As can be seen in the selection of recent articles below from only one journal 'Mitochondrial DNA' there is a significant amount of work being undertaken in this field with respect to avian genetics studies.

Complete mitochondrial genome of Yellow-browed warbler Phylloscopus inornatus inornatus (Passeriformes: Sylviidae)
Posted online on January 10, 2014. 

Hui Qing, et al

Abstract
Yellow-browed warbler Phylloscopus inornatus inornatus (Passeriformes: Sylviidae) is a small insectivorous leaf-gleaning bird which breeds in forests of the east Palaearctic. In this study, we used PCR-based method to determine the complete mitochondrial genome (mtDNA) of this warbler species. The complete mtDNA is a 16,875 bp circular molecule, containing 37 typical genes and an extra pseudo-control region. The gene order differs from the standard gene order in birds, but similar to genus Sylvia and Acrocephalus, which has the remnant CR2 gene order. All protein-coding genes start with a typical ATG codon. The termination codon is usually the standard TAA, but may be TAG (Cyt b and ND6), AGG (COI) or incomplete T-(COIII and ND4). All tRNAs have the typical clover-leaf structure, except the dihydrouridine (DHU) arm of tRNASer (AGN) and tRNALys (CUN), which forms a simple loop. The non-coding region contains some intergenic spacers, a control region and an extra pseudo-control region.

Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.863299

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Complete mitochondrial genome of Germain’s Peacock-Pheasant Polyplectron germaini (Aves, Galliformes, Phasianidae)
Posted online on January 27, 2014. 

Destiny Omeire, et al

Abstract
The Germain’s Peacock-Pheasant Polyplectron germaini (Aves, Galliformes, Phasianidae) is classified as Near Threatened on the IUCN Red List. The complete mitochondrial genome of P. germaini is 16,699 bp, consisting of 13 protein-coding genes, 2 rRNA, 22 tRNA genes and 1 control region. All of the 13 protein-coding genes have ATG as start codon. Eight of the 13 protein-coding genes have TAA as stop codon.

Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.830292

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An effective strategy for species identification of avian meats using the mitochondrial 12S rRNA gene fragment
Posted online on January 27, 2014. 

Lan-Ping Wang, et al

Abstract
An effective DNA-based molecular method had been used to identify avian species from meats. The method combined the use of a pair of universal primers, which amplified about 440-bp fragment of the mitochondrial 12S rRNA gene. A total of 99 meat samples were tested and 17 haplotypes were identified by DNA sequencing, which representing 14 avian species. One avian species was listed as the national first-grade protected animal in China and the IUCN endangered species. Two avian species were under the national second-grade state protection. The proposed method represents a straightforward and robust method for the accurate identification of avian species that could be used by law enforcement agencies as a tool for the control of illegal trade of meat from protected species.


Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.845769

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Complete mitochondrial genome of black grouse (Lyrurus tetrix)
Posted online on January 22, 2014. 

Bo Li1, et al

Abstract
We sequenced the entire mitochondrial genome of Lyrurus tetrix for the first time. The mitogenome was 16,677 bp in length, encoded with a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes plus a putative control region. Almost all genes were encoded on the H-strand except the ND6 and eight tRNA genes. All protein-coding genes initiated with ATG, except for COX1 and ND5 (GTG). An 18-bp-nucleotide deletion occured in the ND6 of Lyrurus tetrix in contrast to other Galliformes. The total base composition of the mitogenome was 30.4% for A, 30.4% for C, 25.8% for T and 13.4% for G. These results provide basic information for phylogenetic analyses among Galliformes.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.878911

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The complete mitochondrial genome sequence of the Daweishan Mini chicken
Posted online on January 22, 2014. 

Ming-Li Yan, et al

Abstract
Daweishan Mini chicken is a valuable chicken breed in China. In this study, the complete mitochondrial genome sequence of Daweishan Mini chicken using PCR amplification, sequencing and assembling has been obtained for the first time. The total length of the mitochondrial genome was 16,785 bp, with the base composition of 30.26% A, 23.73% T, 32.51% C, 13.51% G. It contained 37 genes (2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes) and a major non-coding control region (D-loop region). The protein start codons are ATG, except for COX1 that begins with GTG. The complete mitochondrial genome sequence of Daweishan Mini chicken provides an important data set for further investigation on the phylogenetic relationships within Gallus gallus.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.878913

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The complete mitochondrial genome of Garrulax cineraceus (Aves, Passeriformes, Timaliidae)
Posted online on January 22, 2014. 

Hui Xue, et al

Abstract
The complete sequence of the mitochondrial DNA genome from Garrulax cineraceus was determined using the polymerase chain reaction method. The genome (17,800 bp in length) contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and 2 control regions (D-loop) at two different locations of mitogenome, which is similar to the typical mtDNA of vertebrates. All the protein-coding genes in G. cineraceus were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.878917

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Mitochondrial genome of the Anas crecca (Anatidae: Anas)
Posted online on January 17, 2014. 

Chaochao Hu, et al

Abstract
Mitochondrial DNA plays an important role in living organisms, and has been used as a powerful molecular marker in various evolutionary studies. In this study, we determined the complete mitochondrial genome of Anas crecca (16,601 bp in length). Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Overall base composition of the complete mitochondrial DNA was 29.05% A, 22.35% T, 32.64% C and 15.96% G.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.834434

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The complete mitochondrial genome of the Xuefeng black-boned chicken
Posted online on January 17, 2014. 

Li-Li Liu, et al

Abstract
Xuefeng black-boned chicken is one of the famous native breeds in China. In this work, we reported the complete mitochondrial genome sequence of the Xuefeng black-boned chicken for the first time, which was determined through PCR-based method. The total length of the mitogenome was 16,783 bp, with the base composition of 30.24% for A, 23.72% for T, 32.52% for C, 13.53% for G, in the order C > A > T > G feature occurring in the Xuefeng black-boned chicken. It contained the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). It was similar to the gene arrangement in Silky chicken. The complete mitochondrial genome sequence of the Xuefeng black-boned chicken provided an important data for further study on the genetic mechanism.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.869679

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The complete mitochondrial genome of the Feral Rock Pigeon (Columba livia breed feral)
Posted online on January 17, 2014. 

Chun-Hong Li, et al

Abstract
In the present work, we report the complete mitochondrial genome sequence of feral rock pigeon for the first time. The total length of the mitogenome was 17,239 bp with the base composition of 30.3% for A, 24.0% for T, 31.9% for C, and 13.8% for G and an A–T (54.3 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of feral rock pigeon would serve as an important data set of the germplasm resources for further study.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.873914

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Complete mitochondrial genome of Tundra swan Cygnus columbianus jankowskii (Anseriformes: Anatidae)
Posted online on January 17, 2014. 

Jinghua Wang, et al

Abstract
Cygnus columbianus jankowskii is a subspecies of Tundra swan, which breeds in eastern Russia and northeast China, wintering in the middle and lower reaches of the Yangtze River. In this study, we used PCR-based method to obtain the complete mtDNA of this subspecies. The arrangement pattern of the complete mtDNA is identical with typical bird species, which is the shortest (16,723 bp) in three subspecies. The length of the PCGs is same except ND2, ND3 and ND6, and the initiation/termination codons are all same with other subspecies. The length of 12S rRNA and 16S rRNA is same with C. c. columbianus, but different from C. c. bewickii. The length and structure of all tRNAs are the same with other subspecies except for tRNAIle, tRNAleu(CUN) and tRNAser(AGY). The control region is located between tRNAPhe and tRNAGlu, but the length is different with others.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.873917

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Mitochondrial genome sequence of Egyptian swift Rock Pigeon (Columba livia breed Egyptian swift)
Posted online on January 17, 2014. 

Chun-Hong Li, et al

Abstract
The Egyptian swift Rock Pigeon is a breed of fancy pigeon developed over many years of selective breeding. In this work, we report the complete mitochondrial genome sequence of Egyptian swift Rock Pigeon. The total length of the mitogenome was 17,239 bp and its overall base composition was estimated to be 30.2% for A, 24.0% for T, 31.9% for C and 13.9% for G, indicating an A–T (54.2%)-rich feature in the mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The complete mitochondrial genome sequence of Egyptian swift Rock Pigeon would serve as an important data set of the germplasm resources for further study.



Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.873931

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