The complete chloroplast genome sequence of Asian Palmyra palm (Borassus flabellifer)

Abstract

Objective Borassus flabellifer or Asian Palmyra palm is widely distributed in South and Southeast Asia and is horticultural and economic importance for its fruit and palm sugar production. However, its population is in rapid decline, and only a few genetic data are available. We sequenced the complete chloroplast (cp) genome of B. flabellifer to provide its genetic data for further utilization.ResultsThe cp genome was obtained by Illumina sequencing and manual gap fillings providing 160,021 bp in length containing a pair of inverted repeats (IRs) with 27,256 bp. These IRs divide the genome into a large single copy region 87,444 bp and a small single copy region 18,065 bp. In total, 113 unique genes, 134 SSRs and 47 large repeats were identified. This is the first complete cp genome reported in the genus Borassus. A comparative analysis among members of the Borasseae tribe revealed that the B. flabellifer cp genome is, so far, the largest and the cp genomes of this tribe have a similar structure, gene number and gene arrangement. A phylogenetic tree reconstructed based on 74 protein-coding genes from 70 monocots demonstrates short branch lengths indicating slow evolutionary rates of cp genomes in family Arecaceae.Electronic supplementary materialThe online version of this article (10.1186/s13104-017-3077-8) contains supplementary material, which is available to authorized users.

Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

“…Several methods have been used to sequence chloroplast genomes in plants, including primer walking [11][12][13][14] and high-throughput sequencing (HTS) [15]. HTS, both with isolated chloroplast DNA [16][17][18] and total cellular DNA [19][20][21], has been employed to generate physical maps of the chloroplast genome. However, the junctions of LSC/IRa, IRa/SSC, SSC/IRb and IRb/LSC need to be resolved using additional experimentation [22].…”

RNA editing in the chloroplast of Asian Palmyra palm (Borassus flabellifer)

“…Although we have analyzed 35 cp genes of B. flabellifer for RNA editing, in which 20 genes are positive, the assessment of RNA editing in this species is still far from being complete. There are other 45 out of 79 protein coding genes in the B. flabellifer cp genome left to be analyzed (Sakulsathaporn et al, 2017).…”

“…PCR products were resolved by 1% agarose gel electrophoresis and purified using a gel extraction kit (Flavorgen, Taiwan) before Sanger's sequencing (Macrogen, Korea). The transcription sequences were then aligned against predicted RNA editing and cpDNA (GenBank accession number KP_901247; (Sakulsathaporn et al, 2017) using Clustal Omega.…”

Methods of analysis of Chloroplast Genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

“…Several methods have been used to sequence chloroplast genomes in plants, including primer walking [11][12][13][14] and high-throughput sequencing (HTS) [15]. HTS, both with isolated chloroplast DNA [16][17][18] and total cellular DNA [19][20][21], has been employed to generate physical maps of the chloroplast genome. However, the junctions of LSC/IRa, IRa/SSC, SSC/IRb and IRb/LSC need to be resolved using additional experimentation [22].…”