A study of the peopling of Greenland using next generation sequencing of complete mitochondrial genomes

2016 ◽  
Vol 161 (4) ◽  
pp. 698-704 ◽  
Author(s):  
Maria Lopopolo ◽  
Claus Børsting ◽  
Vania Pereira ◽  
Niels Morling
Keyword(s):  
Next Generation Sequencing ◽  
Mitochondrial Genomes ◽  
Next Generation ◽  
Generation Sequencing ◽  
Complete Mitochondrial Genomes

Characterization of the complete mitochondrial genomes from Polycladida (Platyhelminthes) using next-generation sequencing

Gene ◽  
2016 ◽  
Vol 575 (2) ◽  
pp. 199-205 ◽  
Author(s):  
M. Teresa Aguado ◽  
Cristina Grande ◽  
Michael Gerth ◽  
Christoph Bleidorn ◽  
Carolina Noreña
Keyword(s):  
Next Generation Sequencing ◽  
Mitochondrial Genomes ◽  
Next Generation ◽  
Generation Sequencing ◽  
Complete Mitochondrial Genomes

scholarly journals Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2786 ◽  
Author(s):  
Siqi Yuan ◽  
Yun Xia ◽  
Yuchi Zheng ◽  
Xiaomao Zeng
Keyword(s):  
Next Generation Sequencing ◽  
Gene Order ◽  
Illumina Miseq ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Next Generation ◽  
Protein Coding ◽  
Alignment Errors ◽  
Generation Sequencing

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order,Amolops chunganensisandQuasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome ofA. chunganensisandQ. boulengeriare typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome ofQ. boulengeriis characterized with a tandem duplication oftrnM. Moreover, we utilize 13 protein-coding genes ofA. chunganensis,Q. boulengeriand other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity ofA. chunganensisandQ. boulengeri. In this work, we provide nearly complete mitochondrial genomes ofA. chunganensisandQ. boulengeri.

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