Phoenix dactylifera L.
Information about Date palm Genome
Date palm (Phoenix dactylifera L.), tree of the palm family (Arecaceae or Palmae), was found in the Canary Islands, northern Africa, the Middle East, Pakistan, India, and the U.S. state of California (https://www.britannica.com/plant/date-palm). Date palm is a cultivated woody plant species of agricultural and economic importance in many countries around the world. Individual varieties are valued primarily for fruit-related traits including moisture and sugar content.
The date palm genome GAA (v1.1) has been published in 2012 (Yao et al., 2012) [1], and updated by Hu lab in 2017 (Songnian Hu et al., 2017)[2] using 130X of HiSeq data. The updated genome assembly version (DPV02) release was online on DRDB (http://drdb.big.ac.cn/home), it has the following information:
The date palm genome GAA (v1.1) has been published in 2012 (Yao et al., 2012) [1], and updated by Hu lab in 2017 (Songnian Hu et al., 2017)[2] using 130X of HiSeq data. The updated genome assembly version (DPV02) release was online on DRDB (http://drdb.big.ac.cn/home), it has the following information:
● Assembled genome size (contig size ≥500 bp): 543 Mb
● Number of Unplaced Scaffolds: 50131
● Scaffold Average size (bp): 10834
● N50 (bp): 349197
● Number of Genes: 35035
● Number of transcripts: 350355
● Number of Unplaced Scaffolds: 50131
● Scaffold Average size (bp): 10834
● N50 (bp): 349197
● Number of Genes: 35035
● Number of transcripts: 350355
Genome Re-sequencing Projects and Variation Identification
Recently, dozens of date palm cultivars have been re-sequenced:
● Michael D. Purugganan et al., 2015, 62 date palm cultivars (from 4 region and 10 countries) were resequenced [3].
References
1. Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM: Graph accordance of next-generation sequence assemblies. Bioinformatics 2012, 28(1):13-16. [PMID=22025481]
2. He Z, Zhang C, Liu W, Lin Q, Wei T, Aljohi HA, Chen WH, Hu S: DRDB: An Online Date Palm Genomic Resource Database. Frontiers in plant science 2017, 8:1889. [PMID=29209336]
3. Hazzouri KM, Flowers JM, Visser HJ, Khierallah HS, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD: Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nat Commun 2015, 6:8824. [PMID=26549859]