Date Palm Chloroplast Genome
A research group led by Prof. YU Jun of Beijing Institute of Genomics has recently finished the complete sequence of the date palm chloroplast genome, as a step of the Date Palm Genome Project in cooperation with Saudi Arabia.
Date palm (Phoenix dactylifera L.), a member of Arecaceae family, is one of the three major economically important woody palms—the two other palms being oil palm and coconut tree—and its fruit is a staple food among Middle East and North African nations, as well as many other tropical and subtropical regions. Here the researchers report a complete sequence of the date palm chloroplast (cp) genome based on pyrosequencing.
After extracting 369,022 cp sequencing reads from whole-genome-shotgun data, the researchers put together an assembly and validated it with intensive PCR-based verification, coupled with PCR product sequencing. The date palm cp genome is 158,462 bp in length and has a typical quadripartite structure of the large (LSC, 86,198 bp) and small single-copy (SSC, 17,712 bp) regions separated by a pair of inverted repeats (IRs, 27,276 bp). Similar to what has been found among most angiosperms, the date palm cp genome harbors 112 unique genes and 19 duplicated fragments in the IR regions. The junctions between LSC/IRs and SSC/IRs show different features of sequence expansion in evolution. The researchers identified 78 SNPs as major intravarietal polymorphisms within the population of a specific cp genome, most of which were located in genes with vital functions. Based on RNA-sequencing data, the researchers also found 18 polycistronic transcription units and three highly expression-biased genes—atpF, trnA-UGC, and rrn23.
Unlike most monocots, date palm has a typical cp genome similar to that of tobacco—with little rearrangement and gene loss or gain. High-throughput sequencing technology facilitates the identification of intravarietal variations in cp genomes among different cultivars. Moreover, transcriptomic analysis of cp genes provides clues for uncovering regulatory mechanisms of transcription and translation in chloroplasts.
The article was published in PloS ONE on September 15, 2010. The full text is freely available online at http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012762.
