A precise chloroplast genome of Nelumbo nucifera Nelumbonaceae evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicotsReport as inadecuate




A precise chloroplast genome of Nelumbo nucifera Nelumbonaceae evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots - Download this document for free, or read online. Document in PDF available to download.

BMC Plant Biology

, 14:289

Genomics and evolution

Abstract

BackgroundThe chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II, known as `SMRT Single Molecule, Real-Time sequencing’, has been developed. Using the SMRT sequencing to investigate the chloroplast genome of N. nucifera will help to elucidate the plastid evolution of basal eudicots.

ResultsThe sizes of the de novo assembled complete chloroplast genome of N. nucifera were 163,307 bp, 163,747 bp and 163,600 bp with average depths of coverage of 7×, 712× and 105× sequenced by Sanger, Illumina MiSeq and PacBio RS II, respectively. The precise chloroplast genome of N. nucifera was obtained from PacBio RS II data proofread by Illumina MiSeq reads, with a quadripartite structure containing a large single copy region 91,846 bp and a small single copy region 19,626 bp separated by two inverted repeat regions 26,064 bp. The genome contains 113 different genes, including four distinct rRNAs, 30 distinct tRNAs and 79 distinct peptide-coding genes. A phylogenetic analysis of 133 taxa from 56 orders indicated that Nelumbo with an age of 177 million years is a sister clade to Platanus, which belongs to the basal eudicots. Basal eudicots began to emerge during the early Jurassic with estimated divergence times at 197 million years using MCMCTree. IR expansions-contractions within the basal eudicots seem to have occurred independently.

ConclusionsBecause of long reads and lack of bias in coverage of AT-rich regions, PacBio RS II showed a great promise for highly accurate `finished’ genomes, especially for a de novo assembly of genomes. N. nucifera is one member of basal eudicots, however, evolutionary analyses of IR structural variations of N. nucifera and other basal eudicots suggested that IR expansions-contractions occurred independently in these basal eudicots or were caused by independent insertions and deletions. The precise chloroplast genome of N. nucifera will present new information for structural variation of chloroplast genomes and provide new insight into the evolution of basal eudicots at the primary sequence and structural level.

KeywordsN. nucifera Chloroplast genome sequencing Basal eudicots Systematic position Divergence time PacBio RS II Electronic supplementary materialThe online version of this article doi:10.1186-s12870-014-0289-0 contains supplementary material, which is available to authorized users.

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Author: Zhihua Wu - Songtao Gui - Zhiwu Quan - Lei Pan - Shuzhen Wang - Weidong Ke - Dequan Liang - Yi Ding

Source: https://link.springer.com/







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