The Mitochondrial Genome of an Aquatic Plant, Spirodela polyrhiza

Abstract

Background Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.Methods Spirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method.ConclusionsThis is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs) cover 71,783 bp (31.0%) of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1%) of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into Spirodela mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that Spirodela shares the common ancestor with other monocots, but there is no obvious synteny between Spirodela and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the Spirodela mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot mitochondrial genomes.

The Complete Sequence of the Mitochondrial Genome of Butomus umbellatus – A Member of an Early Branching Lineage of Monocotyledons

“…It is questionable whether these short sequences are indeed remnants of sequences transferred from the nuclear genome, but even if they are they constitute only 0.2% of the mitochondrial genome. This low percentage is consistent with the lack of repetitive elements in the mitochondrial genome of Spirodela [14]. As a supplement to the Repbase Update search we conducted a BLASTN search against GenBank sequences filtering for chloroplast and mitochondrial sequences.…”

“…451 kb the mitochondrial genome of Butomus is almost twice as large as the ca. 228 kb genome of Spirodela [14], the only other genome from the Alismatales sequences so far, but closer in size to the grass genomes ranging from ca. 453–704 kb (Table 1).…”

“…Thus, mitochondrial structure and evolution in the early branching angiosperm lineages remains completely unknown though the sequence of the mitochondrial genome of Amborella , assumed to be the sister group to all other angiosperms, may be under way [13]. In the monocotyledons the only two non-grass genomes are from Spirodela , duckweed, (Araceae) [14] and Phoenix , date palm, (Arecaceae) [15].…”

Callus induction and frond regeneration in Spirodela polyrhiza

“…Being the most primitive, S. polyrhiza, which has the smallest genome size in the family Lemnaceae, is the most frequently studied as an ideal system in biochemical research for bioremediation and carbon cycle ( Wang et al 2012( Wang et al , 2015Kuehdorf et al 2014;Tang et al 2014;Olah et al 2015;Xu et al 2015). doi: 10.17221/134/2015-CJGPB However, no information on a frond regeneration system is available in S. polyrhiza.…”

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

“…Processing of NGS data using standard analysis software has the advantage that all NGS sequence reads contributing to the chloroplast assembly can be processed for variant analysis to identify variants and their frequency at each base position. Although a plant cell has many copies of the chloroplast and mitochondrial genomes, cp-genomes are many times more abundant than mitochondrial genomes (for example, in Arabidopsis leaf, there are 1,000 to 1,700 cpgenomes per cell (Zoschke et al, 2007), and there are about 100 copies of the mitochondrial genomes per cell, depending on the physiological state) (Wang et al, 2012).…”