8月，由中科院北京基因组研究所与沙特王国阿卜杜拉阿齐兹国王科技城（King Abdulaziz City for Science and Technology，KACST）共同开展的“中-沙椰枣基因组计划”取得阶段进展，科研人员于近日完成了椰枣基因组叶绿体的基因组测序与分析工作，相关学术论文在PLoS ONE杂志发表。
自2008年底该项目启动以来，北京基因组所不间断地向沙特国王科技城（KACST）派驻了十余名科研骨干。根据前期合作要求，一年多来，在双方的共同努力下，科研人员已经在KACST建立起了一整套基因组和生物信息学实验平台。此次完成的椰枣叶绿体基因分析即由该平台独立完成，主要是利用新一代454高通量测序仪产出数据，筛选出叶绿体数据，并借助SOLiD Mate-pair数据进行拼接和分析。
同时，该篇学术论文也是中-沙两国椰枣项目合作组成立以来发表的第一篇学术论文。它标志着基因组所与KACST共建的基因组测序与信息平台已经高速运转，并产出高质量的数据和分析结果。
这也是国际上首次发布椰枣的叶绿体基因组数据，对植物特别是棕榈科植物的进化模式研究具有十分重要的意义。（生物谷Bioon.com）
原文摘要：
PLoS ONE doi:10.1371/journal.pone.0012762
The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)
Meng Yang1,2, Xiaowei Zhang1,2, Guiming Liu1,2, Yuxin Yin1,2, Kaifu Chen1,2, Quanzheng Yun1,2, Duojun Zhao1,2, Ibrahim S. Al-Mssallem1,3*, Jun Yu1,2*
1 The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia, 2 Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China, 3 Department of Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Hssa, Hofuf, Kingdom of Saudi Arabia
Background
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 we report a complete sequence of the data palm chloroplast (cp) genome based on pyrosequencing.
Methodology/Principal Findings
After extracting 369,022 cp sequencing reads from our whole-genome-shotgun data, we 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. We 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, we also found 18 polycistronic transcription units and three highly expression-biased genes—atpF, trnA-UGC, and rrn23.
Conclusions
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.
