Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new mitogenomes

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60460709%3A41320%2F19%3AN0000136" target="_blank" >RIV/60460709:41320/19:N0000136 - isvavai.cz</a>

Result on the web

<a href="https://www.nature.com/articles/s41598-019-51313-7" target="_blank" >https://www.nature.com/articles/s41598-019-51313-7</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1038/s41598-019-51313-7" target="_blank" >10.1038/s41598-019-51313-7</a>

Result language

angličtina

Original language name

Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new mitogenomes

Original language description

Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochondria. genomes from RNA-Seq experiments of Reticulitermes termite species, for which transcriptomes and conspecific mitogenomes are available. We successfully assembled complete molecules, although a few gaps corresponding to tRNAs had to be filled manually. We also reconstructed, for the first time, the mitogenome of Reticulitermes banyulensis. The accuracy and completeness of mitogenomes reconstruction appeared independent from transcriptome size, read length and sequencing design (single - paired end), and using reference genomes from congeneric or intra-familial taxa did not significantly affect the assembly. Transcriptome-derived mitogenomes were found highly similar to the conspecific ones obtained from genome sequencing (nucleotide divergence ranging from 0% to 3,5%) and yielded a congruent phylogenetic tree. Reads from contaminants and nuclear transcripts, although slowing down the process, did not result in chimeric sequence reconstruction. We suggest that the described approach has the potential to increase the number of available mitogenomes by exploiting the rapidly increasing number of transcriptomes.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/GJ15-07015Y" target="_blank" >GJ15-07015Y: Resolving the anomalies of global termite distribution patterns</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Scientific Reports

ISSN

2045-2322

e-ISSN

—

Volume of the periodical

9

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

1-9

UT code for WoS article

000490121400024

EID of the result in the Scopus database

2-s2.0-85073458569