8月,，由中科院北京基因組研究所與沙特王國(guó)阿卜杜拉阿齊茲國(guó)王科技城（King Abdulaziz City for Science and Technology，KACST）共同開展的“中-沙椰棗基因組計(jì)劃”取得階段進(jìn)展,，科研人員于近日完成了椰棗基因組葉綠體的基因組測(cè)序與分析工作,，相關(guān)學(xué)術(shù)論文在PLoS ONE雜志發(fā)表。
自2008年底該項(xiàng)目啟動(dòng)以來,，北京基因組所不間斷地向沙特國(guó)王科技城（KACST）派駐了十余名科研骨干,。根據(jù)前期合作要求，一年多來,，在雙方的共同努力下,，科研人員已經(jīng)在KACST建立起了一整套基因組和生物信息學(xué)實(shí)驗(yàn)平臺(tái)。此次完成的椰棗葉綠體基因分析即由該平臺(tái)獨(dú)立完成,，主要是利用新一代454高通量測(cè)序儀產(chǎn)出數(shù)據(jù),，篩選出葉綠體數(shù)據(jù)，并借助SOLiD Mate-pair數(shù)據(jù)進(jìn)行拼接和分析,。
同時(shí),，該篇學(xué)術(shù)論文也是中-沙兩國(guó)椰棗項(xiàng)目合作組成立以來發(fā)表的第一篇學(xué)術(shù)論文。它標(biāo)志著基因組所與KACST共建的基因組測(cè)序與信息平臺(tái)已經(jīng)高速運(yùn)轉(zhuǎn),，并產(chǎn)出高質(zhì)量的數(shù)據(jù)和分析結(jié)果,。
這也是國(guó)際上首次發(fā)布椰棗的葉綠體基因組數(shù)據(jù),，對(duì)植物特別是棕櫚科植物的進(jìn)化模式研究具有十分重要的意義。（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.
