An efficient approach for obtaining plant organelle genomes

Plant organelle(plastid and mitochondrial)genomes contain substantial information for plant evolution and adaptation.Therefore,it’s important to reveal plant whole-genome sequences including plastid and mitochondrial genomes.To decode these sequences,it is required to efficiently separate organelle genomic DNA from nucleus genome,which is difficult and laborious.In this study,an efficient procedure was established to obtain plant organelle genomes without extraction of plastid and mitochondria.Organelle DNA was extracted from three materials including Sinapis arvensis var.‘Yeyou 18’,a cytoplasmic male sterile line(Nsa CMS)and its corresponding maintainer line‘Zhongshuang 4’.DNA was sequenced by Roche 454 FLXt and Illumina Miseq platforms.Organelle genomes were assembled using the generated reads and public organelle genome sequences.This research presented a procedure that efficiently assembled organelle genomes and subsequent fill gaps by extending the consensus contig terminals.This method enabled us to assemble plant plastid and mitochondrial genomes simultaneously.The obtained organelle genomes could accelerate understanding of mitochondrial rearrangements and laid a foundation for further study of Sinapis arvensis evolution and sterility gene of Nsa CMS.

Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia(Florideophyceae,Rhodophyta)

Hildenbrandia is an early diverged lineage in Florideophyceae,Rhodophyta.The species diversity of this genus is still unresolved due to the simple morphology and limited molecular information.The mitochondrial genome of freshwater H.jigongshanensis was determined in this study.The freshwater H.jigongshanensis had a larger mitochondrial genome than the marine H.rubra and GC content was higher.Collinear alignment structure was observed between the mitochondrial genomes of H.jigongshanensis and H.rubra,except for one block that was encoded on the complement strand.More introns were found in mitochondrial genome of H.jigongshanensis than in H.rubra,and H.jigongshanensis shares the common feature with Bangiophyceae that two introns were distributed in cox1.Comparison of mitochondrial genome organization suggests that H.jigongshanensis preserves characters that could be hypothetically more similar to the ancestor of Bangiophyceae and Florideophyceae,which differ with previous studies based on chloroplast,and nuclear markers.More mitochondrial genomes and phylogenetic analyses combing nuclear,chloroplast and mitochondrial genomes are needed to clarify this discrepancy.Mitochondrion-based phylogeny in this study resulted in better solution at both the deep and recent derived nodes than single-gene phylogenies.Most protein-coding genes between H.jigongshanensis and H.rubra were identical except atp8,which was present in H.jigongshanensis while absent from H.rubra.This finding follows the trend that high Ka/Ks ratio genes are more frequently lost than low Ka/Ks ratio ones in red algae.