the complete chloroplast genome sequence of date palm (phoenix dactylifera l.)枣椰树的完整叶绿体基因组序列(凤凰dactylifera l .).pdf

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* 1The 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 Abstract 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 wi