Abstract
Date palm is one of the most economically important woody crops cultivated in the Middle East and North Africa and is a good candidate for improving agricultural yields in arid environments. Nonetheless, long generation times (5-8 years) and dioecy (separate male and female trees) have complicated its cultivation and genetic analysis. To address these issues, we assembled a draft genome for a Khalas variety female date palm, the first publicly available resource of its type for a member of the order Arecales. The 1/4380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover 1/490% of genes and 1/460% of the genome. Sequencing of eight other cultivars, including females of the Deglet Noor and Medjool varieties and their backcrossed males, identified >3.5 million polymorphic sites, including >10,000 genic copy number variations. A small subset of these polymorphisms can distinguish multiple varieties. We identified a region of the genome linked to gender and found evidence that date palm employs an XY system of gender inheritance.
| Original language | English |
|---|---|
| Pages (from-to) | 521-527 |
| Number of pages | 7 |
| Journal | Nature Biotechnology |
| Volume | 29 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - Jun 2011 |
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ASJC Scopus subject areas
- Applied Microbiology and Biotechnology
- Biotechnology
- Molecular Medicine
- Bioengineering
- Biomedical Engineering
Cite this
De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). / Aldous, Eman; George, Binu; Al-Mahmoud, Maryam E.; Al-Jaber, Moneera Y.; Wang, Hao; Salameh, Yasmeen M.; Al-Azwani, Eman K.; Chaluvadi, Srinivasa; Pontaroli, Ana C.; Debarry, Jeremy; Arondel, Vincent; Ohlrogge, John; Saie, Imad J.; Suliman-Elmeer, Khaled M.; Bennetzen, Jeffrey L.; Kruegger, Robert R.; Malek, Joel.
In: Nature Biotechnology, Vol. 29, No. 6, 06.2011, p. 521-527.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)
AU - Aldous, Eman
AU - George, Binu
AU - Al-Mahmoud, Maryam E.
AU - Al-Jaber, Moneera Y.
AU - Wang, Hao
AU - Salameh, Yasmeen M.
AU - Al-Azwani, Eman K.
AU - Chaluvadi, Srinivasa
AU - Pontaroli, Ana C.
AU - Debarry, Jeremy
AU - Arondel, Vincent
AU - Ohlrogge, John
AU - Saie, Imad J.
AU - Suliman-Elmeer, Khaled M.
AU - Bennetzen, Jeffrey L.
AU - Kruegger, Robert R.
AU - Malek, Joel
PY - 2011/6
Y1 - 2011/6
N2 - Date palm is one of the most economically important woody crops cultivated in the Middle East and North Africa and is a good candidate for improving agricultural yields in arid environments. Nonetheless, long generation times (5-8 years) and dioecy (separate male and female trees) have complicated its cultivation and genetic analysis. To address these issues, we assembled a draft genome for a Khalas variety female date palm, the first publicly available resource of its type for a member of the order Arecales. The 1/4380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover 1/490% of genes and 1/460% of the genome. Sequencing of eight other cultivars, including females of the Deglet Noor and Medjool varieties and their backcrossed males, identified >3.5 million polymorphic sites, including >10,000 genic copy number variations. A small subset of these polymorphisms can distinguish multiple varieties. We identified a region of the genome linked to gender and found evidence that date palm employs an XY system of gender inheritance.
AB - Date palm is one of the most economically important woody crops cultivated in the Middle East and North Africa and is a good candidate for improving agricultural yields in arid environments. Nonetheless, long generation times (5-8 years) and dioecy (separate male and female trees) have complicated its cultivation and genetic analysis. To address these issues, we assembled a draft genome for a Khalas variety female date palm, the first publicly available resource of its type for a member of the order Arecales. The 1/4380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover 1/490% of genes and 1/460% of the genome. Sequencing of eight other cultivars, including females of the Deglet Noor and Medjool varieties and their backcrossed males, identified >3.5 million polymorphic sites, including >10,000 genic copy number variations. A small subset of these polymorphisms can distinguish multiple varieties. We identified a region of the genome linked to gender and found evidence that date palm employs an XY system of gender inheritance.
UR - http://www.scopus.com/inward/record.url?scp=79958165589&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79958165589&partnerID=8YFLogxK
U2 - 10.1038/nbt.1860
DO - 10.1038/nbt.1860
M3 - Article
C2 - 21623354
AN - SCOPUS:79958165589
VL - 29
SP - 521
EP - 527
JO - Nature Biotechnology
JF - Nature Biotechnology
SN - 1087-0156
IS - 6
ER -