Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis
| Autor: | Shao-quan Zheng, Wenshun Hu, Chen Xiuping, Jiang Fan |
|---|---|
| Jazyk: | angličtina |
| Předmět: |
Peel color
0106 biological sciences 0301 basic medicine Genetics Candidate gene Multidisciplinary Differentially expressed genes (DEGs) biology Sequence database Protein family genetic structures Sequence analysis Research Anthocyanins (ACs) biology.organism_classification 01 natural sciences 03 medical and health sciences Dimocarpus confinis 030104 developmental biology KEGG Gene 010606 plant biology & botany Regulator gene |
| Zdroj: | SpringerPlus |
| ISSN: | 2193-1801 |
| DOI: | 10.1186/s40064-016-2743-y |
| Popis: | Nowadays, there are few reports about regulatory genes implicated in peel color of longan. The basic genetic research of longan has been in stagnation for a long time as a lack of transcriptomic and genetic information. To predict candidate genes associated with peel color, Gene Functional Annotation and Coding Sequence prediction were used to perform functional annotation for our assembled unigenes and investigate differentially expressed genes (DEGs) of fruitlet peels from Longli (Dimocarpus confinis). Finally, a total of 24,044 (44.19 %) unigenes were annotated at least in one database after BLAST search to NCBI non-redundant protein sequence, NCBI non-redundant nucleotide sequences, Kyoto Encyclopedia of Genes and Genomes (KEGG) Ortholog, manually annotated and reviewed protein sequence database (Swiss-Prot), Protein family, Gene Ontology, euKaryotic Ortholog Groups databases. After searching against the KEGG-GENE protein database, a result of 6228 (11.45 %) unigenes were assigned to 245 KEGG pathways. Via comparing the distributions of expression value of all corresponding unigenes from red peel and green peel fruit, it could be intuitively concluded that high similarity was existed in the two distributions; however, on the whole, between two distributions of log RPKM expression value, some differences indicated that expression level in green-peel fruit group is slightly higher than values in red-peel fruit group. Finally, a total of 1349 unigenes were identified as DEGs after blasting the DEGs to public sequence databases, and 32 peel-color-related genes were identified in longan. Our results suggest that a number of unigenes involved in longan metabolic process, including anthocyanin biosynthesis. In addition, DRF, F3H, ANS, CYP75A1 and C1 may be the key ones. The study on key genes related to peel color will be contributed to revealing the molecular mechanisms of regulating peel color in woody plants. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2743-y) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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