Dataset Information

Transcription of nuclear organellar DNA in a model plant system.

ABSTRACT: Endosymbiotic gene transfer from cytoplasmic organelles (chloroplasts and mitochondria) to the nucleus is an ongoing process in land plants. Although the frequency of organelle DNA migration is high, functional gene transfer is rare because a nuclear promoter is thought necessary for activity in the nucleus. Here we show that a chloroplast promoter, 16S rrn, drives nuclear transcription, suggesting that a transferred organellar gene may become active without obtaining a nuclear promoter. Examining the chromatin status of a known de novo chloroplast integrant indicates that plastid DNA inserts into open chromatin and that this relaxed condition is maintained after integration. Transcription of nuclear organelle DNA integrants was explored at the whole genome level by analyzing RNA-seq data of Oryza sativa subsp. japonica, and utilizing sequence polymorphisms to unequivocally discriminate nuclear organelle DNA transcripts from those of bona fide cytoplasmic organelle DNA. Nuclear copies of organelle DNA that are transcribed show a spectrum of transcriptional activity but at comparatively low levels compared with the majority of other nuclear genes.

SUBMITTER: Wang D

PROVIDER: S-EPMC4079196 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Transcription of nuclear organellar DNA in a model plant system.

Wang Dong D Qu Zhipeng Z Adelson David L DL Zhu Jian-Kang JK Timmis Jeremy N JN

Genome biology and evolution 20140527 6

Endosymbiotic gene transfer from cytoplasmic organelles (chloroplasts and mitochondria) to the nucleus is an ongoing process in land plants. Although the frequency of organelle DNA migration is high, functional gene transfer is rare because a nuclear promoter is thought necessary for activity in the nucleus. Here we show that a chloroplast promoter, 16S rrn, drives nuclear transcription, suggesting that a transferred organellar gene may become active without obtaining a nuclear promoter. Examini ...[more]

PMID: 24868015

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Project description:Background and aimsSphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.MethodsWe obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and FlatbergiumKey resultsPhylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and FlatbergiumConclusionsNewly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.

Dataset Information

Transcription of nuclear organellar DNA in a model plant system.

Publications

Transcription of nuclear organellar DNA in a model plant system.

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