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Mapping 3′ transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq

Overview of attention for article published in BMC Genomics, October 2015
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Title
Mapping 3′ transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-2103-2
Pubmed ID
Authors

Silvia Marková, Karolína Filipi, Jeremy B. Searle, Petr Kotlík

Abstract

Although posttranscriptional modification of mitochondrial (mt) transcripts plays key roles in completion of the coding information and in the expression of mtDNA-encoded genes, there is little experimental evidence on the polyadenylation status and the location of mt gene poly(A) sites for non-human mammals. Poly(A)-enriched RNA-Seq reads collected for two wild-caught bank voles (Clethrionomys glareolus) were mapped to the complete mitochondrial genome of that species. Transcript polyadenylation was detected as unmapped adenine residues at the ends of the mapped reads. Where the tRNA punctuation model applied, there was the expected polyadenylation, except for the nad5 transcript, whose polyadenylated 3' end is at an intergenic sequence/cytochrome b boundary. As in human, two pairs of bank vole genes, nad4l/nad4 and atp8/atp6, are expressed from bicistronic transcripts. TAA stop codons of four bank vole protein-coding genes (nad1, atp6, cox3 and nad4) are incompletely encoded in the DNA and are completed by polyadenylation. This is three genes (nad2, nad3 and cob) less than in human. The bank vole nad2 gene encodes a full stop codon (TAA in one vole and TAG in the other), which is followed by a 2 bp UTR and the gene conforms to the tRNA punctuation model. In contrast, the annotations of the reference mouse and some other rodent mt genomes in GenBank include complete TAG stop codons in both nad1 and nad2, which overlap downstream trnI and trnW, respectively. Thus the RNA-Seq data of bank voles provides a model for stop codons of mt-encoded genes in mammals comparable to humans, but at odds with some of the interpretation based purely on genomic data in mouse and other rodents. This work demonstrates how RNA-Seq data were useful to recover mtDNA transcriptome data in a non-model rodent and to shed more light on mammalian mtDNA transcriptome and post-transcriptional modification. Even though gene content and organisation of mtDNA are strongly conserved among mammals, annotations that neglect the transcriptome may be prone to errors in relation to the stop codons.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Czechia 1 6%
Unknown 17 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 4 22%
Student > Bachelor 3 17%
Student > Ph. D. Student 3 17%
Other 2 11%
Student > Doctoral Student 1 6%
Other 3 17%
Unknown 2 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 6 33%
Biochemistry, Genetics and Molecular Biology 3 17%
Chemistry 3 17%
Environmental Science 2 11%
Computer Science 1 6%
Other 0 0%
Unknown 3 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 October 2015.
All research outputs
#9,813,699
of 16,638,522 outputs
Outputs from BMC Genomics
#4,744
of 9,107 outputs
Outputs of similar age
#136,783
of 288,019 outputs
Outputs of similar age from BMC Genomics
#589
of 996 outputs
Altmetric has tracked 16,638,522 research outputs across all sources so far. This one is in the 39th percentile – i.e., 39% of other outputs scored the same or lower than it.
So far Altmetric has tracked 9,107 research outputs from this source. They receive a mean Attention Score of 4.3. This one is in the 43rd percentile – i.e., 43% of its peers scored the same or lower than it.
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