The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)
| Autor: | Yuxin Yin, Xiaowei Zhang, Meng Yang, Duojun Zhao, Guiming Liu, Quanzheng Yun, Jun Yu, Kaifu Chen, Ibrahim S. Al-Mssallem |
|---|---|
| Rok vydání: | 2010 |
| Předmět: |
Genome evolution
Chloroplasts Molecular Sequence Data Population lcsh:Medicine Genomics Arecaceae Genome Genetics and Genomics/Plant Genetics and Gene Expression Molecular Biology/Bioinformatics Complete sequence Gene Expression Regulation Plant Genetics and Genomics/Genomics Genome Chloroplast lcsh:Science education Genetics Whole genome sequencing education.field_of_study Multidisciplinary Base Sequence biology lcsh:R food and beverages Genetics and Genomics/Bioinformatics biology.organism_classification Genetics and Genomics/Genome Projects Plant Biology/Plant Genomes and Evolution RNA Plant Phoenix dactylifera Nucleic Acid Conformation lcsh:Q Genome Plant Research Article |
| Zdroj: | PLoS ONE, Vol 5, Iss 9, p e12762 (2010) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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