High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.)

Date palm provides both staple food and gardening for the Middle East and North African countries for thousands of years. Its fruits have diversified significantly, such as nutritional content, size, length, weight color, and ripping process. Dates palm represent an excellent model system for the st...

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Bibliographic Details
Published in:Plant molecular biology 2012-04, Vol.78 (6), p.617-626
Main Authors: Yin, Yuxin, Zhang, Xiaowei, Fang, Yongjun, Pan, Linlin, Sun, Gaoyuan, Xin, Chengqi, Ba Abdullah, Mohammed M., Yu, Xiaoguang, Hu, Songnian, Al-Mssallem, Ibrahim S., Yu, Jun
Format: Article
Language:English
Subjects:
Arecaceae - genetics
Arecaceae - growth & development
Arecaceae - metabolism
Biochemistry
Biomedical and Life Sciences
Carbohydrate metabolism
Carbohydrate Metabolism - genetics
Cell division
Color
Databases, Genetic
Developmental stages
Enzymes
Expressed Sequence Tags
Food
Fruit - genetics
Fruit - growth & development
Fruits
Gene Expression Profiling
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Genes, Plant
High-Throughput Screening Assays
Life Sciences
Metabolic Networks and Pathways - genetics
Metabolic pathways
Nutrition
Phoenix dactylifera
Plant Pathology
Plant Sciences
Ripening
RNA, Plant - genetics
Starch
Sugar
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Summary:Date palm provides both staple food and gardening for the Middle East and North African countries for thousands of years. Its fruits have diversified significantly, such as nutritional content, size, length, weight color, and ripping process. Dates palm represent an excellent model system for the study of fruit development and diversity of fruit-bearing palm species that produce the most versatile fruit types as compared to other plant families. Using Roche/454 GS FLX instrument, we acquired 7.6 million sequence tags from seven fruiting stages (F1–F7). Over 99% of the raw reads are assembled, and the numbers of isotigs (equivalent to transcription units or unigenes) range from 30,684 to 40,378 during different fruiting stages. We annotated isotigs using BLASTX and BLASTN, and mapped 74% of the isotigs to known functional sequences or genes. Based on gene ontology categorization and pathway analysis, we have identified 10 core cell division genes, 18 ripening related genes, and 7 starch metabolic enzymes, which are involved as nutrition storage and sugar/starch metabolisms. We noticed that many metabolic pathways vary significantly during fruit development, and carbohydrate metabolism (especially sugar synthesis) is particularly prominent during fruit ripening. Transcriptomics study on various fruiting stages of date palm shows complicated metabolic activities during fruit development, ripening, synthesis and accumulation of starch enzymes and other related sugars. Most Genes are highly expressed in early stages of development, while late developmental stages are critical for fruit ripening including most of the metabolism associated ones.
ISSN:0167-4412
1573-5028
DOI:10.1007/s11103-012-9890-5