title: High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.).
abstract: 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.
authors.affiliation: Joint Center for Genomics Research-JCGR, King Abdulaziz City for Science and Technology-KACST and Chinese Academy of Sciences-CAS, Riyadh, Kingdom of Saudi Arabia.
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Yin
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhang
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Fang
authors.forename: Linlin
authors.initials: L
authors.lastname: Pan
authors.forename: Gaoyuan
authors.initials: G
authors.lastname: Sun
authors.forename: Chengqi
authors.initials: C
authors.lastname: Xin
authors.forename: Mohammed M
authors.initials: MM
authors.lastname: Ba Abdullah
authors.forename: Xiaoguang
authors.initials: X
authors.lastname: Yu
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Ibrahim S
authors.initials: IS
authors.lastname: Al-Mssallem
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D028023:Arecaceae / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D050260:Carbohydrate Metabolism / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D057166:High-Throughput Screening Assays; D053858:Metabolic Networks and Pathways / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics
chemical_list: D018749:RNA, Plant