Analysis of expressed sequence tags from oil palm (<i>Elaeis guineensis</i>)

Jouannic, Stéfan; Argout, Xavier; Lechauve, Frédéric; Fizames, Cécile; Borgel, Alain; Morcillo, Fabienne; Aberlenc-Bertossi, Frédérique; Duval, Yves; Tregear, James

doi:10.1016/j.febslet.2005.03.093

Cited by 52 publications

(38 citation statements)

References 20 publications

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“…This higher protein sequence similarity between the two less phylogenetically related plants (the monocotyledonous date palm and the eudicotyledonous grapevine) has been observed by others in gene families from oil palm 18 and for oil palm ESTs 19 . Initial suggestions are that the grasses are a more diverged monocotyledonous group than date palm; however, additional studies will be required to fully explain this observation.…”

Section: Genome Annotationmentioning

confidence: 89%

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

et al. 2011

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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 ~380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover ~90% of genes and ~60% 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.

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Section: Genome Annotationmentioning

confidence: 89%

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

et al. 2011

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“…Scale bars 100 lm for a and b; 400 lm for c; 2 mm for d with M13 Reverse primer. The sequences were then subjected to an automated procedure to verify cleanse, store and analyze sequences (Jouannic et al 2005). The average read length for the two EST populations was approximately 550 bp.…”

Section: Est Generation Analysis and Annotationmentioning

confidence: 99%

Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development

et al. 2009

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With the aim of understanding the molecular mechanisms underlying somatic embryogenesis (SE) in oil palm, we examined transcriptome changes that occur when embryogenic suspension cells are initiated to develop somatic embryos. Two reciprocal suppression subtractive hybridization (SSH) libraries were constructed from oil palm embryogenic cell suspensions: one in which embryo development was blocked by the presence of the synthetic auxin analogue 2,4-dichlorophenoxyacetic acid (2,4-D: ) in the medium (proliferation library); and another in which cells were stimulated to form embryos by the removal of 2,4-D: from the medium (initiation library). A total of 1867 Expressed Sequence Tags (ESTs) consisting of 1567 potential unigenes were assembled from the two libraries. Functional annotation indicated that 928 of the ESTs correspond to proteins that have either no similarity to sequences in public databases or are of unknown function. Gene Ontology (GO) terms assigned to the two EST populations give clues to the underlying molecular functions, biological processes and cellular components involved in the initiation of embryo development. Macroarrays were used for transcript profiling the ESTs during SE. Hierarchical cluster analysis of differential transcript accumulation revealed 4 distinct profiles containing a total of 192 statistically significant developmentally regulated transcripts. Similarities and differences between the global results obtained with in vitro systems from dicots, monocots and gymnosperms will be discussed.

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“…However, genetic improvement of oil palm via conventional breeding is very slow because each selection cycle lasts for around 10 years. As a consequence of the biological characteristics of oil palm (long life cycle and no natural vegetative reproduction) and a high heterogeneity prevalent among hybrids, breeding strategies are labor intensive and time consuming [5,6]. Moreover, planting materials at present are derived from a narrow gene pool, which provides breeders with limited genetic variability for improvement [3].…”

Section: Introductionmentioning

confidence: 99%

A Novel Transcript of Oil Palm (Elaeis guineensis Jacq.), Eg707, is Specifically Upregulated in Tissues Related to Totipotency

et al. 2010

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In this study, we report the molecular characterization of clone Eg707 isolated from cell suspension culture of the oil palm. The deduced polypeptide of clone Eg707 is highly similar to an unknown protein from Arabidopsis thaliana. The presence of an Ald-Xan-dh-C2 superfamily domain in the deduced protein sequence suggested that Eg707 protein might be involved in abscisic acid biosynthesis. Eg707 might be present as a single copy gene in the oil palm genome. This gene is highly expressed in tissue cultured materials compared to vegetative and reproductive tissues, suggesting a role of this gene during oil palm somatic embryogenesis or at the early stages of embryo development. Expression analysis of Eg707 by RNA in situ hybridization showed that Eg707 transcripts were present throughout somatic embryo development starting from proembryo formation at the embryogenic callus stages till the maturing embryo stages. Since proembryo formation within the embryogenic callus is one of the first key factors in oil palm somatic embryo development, it is suggested that Eg707 could be used as a reliable molecular marker for detecting early stage of oil palm somatic embryogenesis.

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Analysis of expressed sequence tags from oil palm (Elaeis guineensis)

Cited by 52 publications

References 20 publications

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development

A Novel Transcript of Oil Palm (Elaeis guineensis Jacq.), Eg707, is Specifically Upregulated in Tissues Related to Totipotency

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