Keeping it complicated: Mitochondrial genome plasticity across diplonemids

Scientific Reports
Matus ValachGertraud Burger

Abstract

Chromosome rearrangements are important drivers in genome and gene evolution, with implications ranging from speciation to development to disease. In the flagellate Diplonema papillatum (Euglenozoa), mitochondrial genome rearrangements have resulted in nearly hundred chromosomes and a systematic dispersal of gene fragments across the multipartite genome. Maturation into functional RNAs involves separate transcription of gene pieces, joining of precursor RNAs via trans-splicing, and RNA editing by substitution and uridine additions both reconstituting crucial coding sequence. How widespread these unusual features are across diplonemids is unclear. We have analyzed the mitochondrial genomes and transcriptomes of four species from the Diplonema/Rhynchopus clade, revealing a considerable genomic plasticity. Although gene breakpoints, and thus the total number of gene pieces (~80), are essentially conserved across this group, the number of distinct chromosomes varies by a factor of two, with certain chromosomes combining up to eight unrelated gene fragments. Several internal protein-coding gene pieces overlap substantially, resulting, for example, in a stretch of 22 identical amino acids in cytochrome c oxidase subunit 1 and NADH de...Continue Reading

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Citations

Mar 29, 2018·Scientific Reports·Kristína ZáhonováMarek Eliáš
Jun 12, 2018·Wiley Interdisciplinary Reviews. RNA·Sara L ZimmerLaurie K Read
Oct 7, 2018·IUBMB Life·Julius LukešJohn M Archibald
Sep 1, 2018·The Journal of Biological Chemistry·Matus ValachGertraud Burger
Oct 8, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jeremy G WidemanThomas A Richards
Jan 11, 2020·Nucleic Acids Research·Binnypreet KaurJulius Lukeš
Mar 12, 2020·Molecular Biology and Evolution·Michael J HammondJulius Lukeš
Oct 12, 2018·IUBMB Life·Gertraud Burger, Matus Valach
Feb 23, 2020·Protist·Ingrid Škodová-SverákováJulius Lukeš

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Datasets Mentioned

BETA
PRJNA392339

Methods Mentioned

BETA
PCR
amplicon sequencing
deamination
RNA-Seq
DNA-Seq
Illumina sequencing

Software Mentioned

MAFFT
BLAST
T SelectVariants
Geneious
Phylobayes
isec
mitoTranscriptomeReconstruction py
BBMerge
BLAT
MrBayes

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