Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

Abstract

BackgroundPineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the most important species in the Bromeliaceae family and is largely traded for fresh fruit consumption. Here, we report the complete chloroplast sequence of the MD-2 pineapple that was sequenced using the PacBio sequencing technology.ResultsIn this study, the high error rate of PacBio long sequence reads of A. comosus’s total genomic DNA were improved by leveraging on the high accuracy but short Illumina reads for error-correction via the latest error correction module from Novocraft. Error corrected long PacBio reads were assembled by using a single tool to produce a contig representing the pineapple chloroplast genome. The genome of 159,636 bp in length is featured with the conserved quadripartite structure of chloroplast containing a large single copy region (LSC) with a size of 87,482 bp, a small single copy region (SSC) with a size of 18,622 bp and two inverted repeat regions (IRA and IRB) each with the size of 26,766 bp. Overall, the genome contained 117 unique coding regions and 30 were repeated in the IR region with its genes contents, structure and arrangement similar to its sister taxon, Typha latifolia. A total of 35 repeats structure were detected in both the coding and non-coding regions with a majority being tandem repeats. In addition, 205 SSRs were detected in the genome with six protein-coding genes contained more than two SSRs. Comparative chloroplast genomes from the subclass Commelinidae revealed a conservative protein coding gene albeit located in a highly divergence region. Analysis of selection pressure on protein-coding genes using Ka/Ks ratio showed significant positive selection exerted on the rps7 gene of the pineapple chloroplast with P less than 0.05. Phylogenetic analysis confirmed the recent taxonomical relation among the member of commelinids which support the monophyly relationship between Arecales and Dasypogonaceae and between Zingiberales to the Poales, which includes the A. comosus.ConclusionsThe complete sequence of the chloroplast of pineapple provides insights to the divergence of genic chloroplast sequences from the members of the subclass Commelinidae. The complete pineapple chloroplast will serve as a reference for in-depth taxonomical studies in the Bromeliaceae family when more species under the family are sequenced in the future. The genetic sequence information will also make feasible other molecular applications of the pineapple chloroplast for plant genetic improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0587-1) contains supplementary material, which is available to authorized users.

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

“…Here too leucine (2264 codons, 9.05%) is the most abundant amino acid and cysteine (416 codons, 1.66%) is the least abundant amino acid (Supplementary Tables S2, S3). Leucine and cysteine are reported as the most and least abundant amino acids respectively in other cp genomes also (Chen et al, 2015; Curci et al, 2015; Redwan et al, 2015). It has been suggested in previous studies that there is a significant relationship between codon usage bias and gene expression level (Iannacone et al, 1997; Rouwendal et al, 1997), therefore it implies that there is a strong natural selection pressure on highly expressed genes to optimize their translation efficiency by using major codons (Bulmer, 1988).…”

Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions

“…Tandem repeat structures are common in chloroplast sequences in both coding and non-coding regions and it would be interesting to capture multimeric nucleotide variations if any are found in C. cayetanensis apicoplasts. Due to its polymorphic nature and co-dominant mode of inheritance, these repeat stretches have been used as DNA markers for population genetics studies [34–37]. The biological significance of this finding in C. cayetanensis remains unknown.…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…These regions are conserved regions of clustered variation called hotspots, containing SNPs and indels [25,26]. The rpoC2, rpoC1, and ycf1 genes are known as hotspots for variation [9,25,26,40]. Therefore, Fritillaria cp genomes contain general hotspot regions for genetic variation as in other land plants.…”

“…Previous studies reported similar divergent regions [6]. These regions are conserved regions of clustered variation called hotspots, containing single-nucleotide polymorphisms (SNPs) and indels [25,26]. The nucleotide variability (Pi) was calculated to show divergence at the sequence level of Fritillaria cp genomes.…”