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Identification of regulatory genes implicated in continuous flowering of longan (Dimocarpus longan L.).

Jia T, Wei D, Meng S, Allan AC, Zeng L - PLoS ONE (2014)

Bottom Line: In addition, 107 flowering-time genes were identified in longan, their expression levels between two longan samples were compared by RPKM method, of which the expression levels of 15 were confirmed by real-time quantitative PCR.Our results suggest longan homologues of SHORT VEGETATIVE PHASE (SVP), GIGANTEA (GI), F-BOX 1 (FKF1) and EARLY FLOWERING 4 (ELF4) may be involved this flowering trait and ELF4 may be a key gene.The identification of candidate genes related to continuous flowering will provide new insight into the molecular process of regulating flowering time in woody plants.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China.

ABSTRACT
Longan (Dimocarpus longan L.) is a tropical/subtropical fruit tree of significant economic importance in Southeast Asia. However, a lack of transcriptomic and genomic information hinders research on longan traits, such as the control of flowering. In this study, high-throughput RNA sequencing (RNA-Seq) was used to investigate differentially expressed genes between a unique longan cultivar 'Sijimi'(S) which flowers throughout the year and a more typical cultivar 'Lidongben'(L) which flowers only once in the season, with the aim of identifying candidate genes associated with continuous flowering. 36,527 and 40,982 unigenes were obtained by de novo assembly of the clean reads from cDNA libraries of L and S cultivars. Additionally 40,513 unigenes were assembled from combined reads of these libraries. A total of 32,475 unigenes were annotated by BLAST search to NCBI non-redundant protein (NR), Swiss-Prot, Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Of these, almost fifteen thousand unigenes were identified as significantly differentially expressed genes (DEGs) by using Reads Per kb per Million reads (RPKM) method. A total of 6,415 DEGs were mapped to 128 KEGG pathways, and 8,743 DEGs were assigned to 54 Gene Ontology categories. After blasting the DEGs to public sequence databases, 539 potential flowering-related DEGs were identified. In addition, 107 flowering-time genes were identified in longan, their expression levels between two longan samples were compared by RPKM method, of which the expression levels of 15 were confirmed by real-time quantitative PCR. Our results suggest longan homologues of SHORT VEGETATIVE PHASE (SVP), GIGANTEA (GI), F-BOX 1 (FKF1) and EARLY FLOWERING 4 (ELF4) may be involved this flowering trait and ELF4 may be a key gene. The identification of candidate genes related to continuous flowering will provide new insight into the molecular process of regulating flowering time in woody plants.

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The top 20 pathway assignments of DEGs based on KEGG.The x-axis indicates the number of DEGs in a category. The y-axis from bottom to top shows the top 20 pathways.
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pone-0114568-g005: The top 20 pathway assignments of DEGs based on KEGG.The x-axis indicates the number of DEGs in a category. The y-axis from bottom to top shows the top 20 pathways.

Mentions: Pathway-based analysis helps to further understand the product of a genes biological function. 14,913 of DEGs were mapped to the KEGG database, a total of 128 different pathways were found in this study related to 6,415 unigenes (Table S2). The maps with highest unigene representation were metabolic pathways (1,625 unigenes), followed by the biosynthesis of secondary metabolites (769 unigenes). Lipid metabolism, glycerophospholipid metabolism, pentose and glucuronate interconversions, oxidative phosphorylation and the spliceosome were included in the top 20 pathways (Figure 5). Specific pathways were found that are implicated in flowering, such as plant hormone signal transduction, the spliceosome, circadian rhythm, and starch and sucrose metabolism.


Identification of regulatory genes implicated in continuous flowering of longan (Dimocarpus longan L.).

Jia T, Wei D, Meng S, Allan AC, Zeng L - PLoS ONE (2014)

The top 20 pathway assignments of DEGs based on KEGG.The x-axis indicates the number of DEGs in a category. The y-axis from bottom to top shows the top 20 pathways.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257721&req=5

pone-0114568-g005: The top 20 pathway assignments of DEGs based on KEGG.The x-axis indicates the number of DEGs in a category. The y-axis from bottom to top shows the top 20 pathways.
Mentions: Pathway-based analysis helps to further understand the product of a genes biological function. 14,913 of DEGs were mapped to the KEGG database, a total of 128 different pathways were found in this study related to 6,415 unigenes (Table S2). The maps with highest unigene representation were metabolic pathways (1,625 unigenes), followed by the biosynthesis of secondary metabolites (769 unigenes). Lipid metabolism, glycerophospholipid metabolism, pentose and glucuronate interconversions, oxidative phosphorylation and the spliceosome were included in the top 20 pathways (Figure 5). Specific pathways were found that are implicated in flowering, such as plant hormone signal transduction, the spliceosome, circadian rhythm, and starch and sucrose metabolism.

Bottom Line: In addition, 107 flowering-time genes were identified in longan, their expression levels between two longan samples were compared by RPKM method, of which the expression levels of 15 were confirmed by real-time quantitative PCR.Our results suggest longan homologues of SHORT VEGETATIVE PHASE (SVP), GIGANTEA (GI), F-BOX 1 (FKF1) and EARLY FLOWERING 4 (ELF4) may be involved this flowering trait and ELF4 may be a key gene.The identification of candidate genes related to continuous flowering will provide new insight into the molecular process of regulating flowering time in woody plants.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China.

ABSTRACT
Longan (Dimocarpus longan L.) is a tropical/subtropical fruit tree of significant economic importance in Southeast Asia. However, a lack of transcriptomic and genomic information hinders research on longan traits, such as the control of flowering. In this study, high-throughput RNA sequencing (RNA-Seq) was used to investigate differentially expressed genes between a unique longan cultivar 'Sijimi'(S) which flowers throughout the year and a more typical cultivar 'Lidongben'(L) which flowers only once in the season, with the aim of identifying candidate genes associated with continuous flowering. 36,527 and 40,982 unigenes were obtained by de novo assembly of the clean reads from cDNA libraries of L and S cultivars. Additionally 40,513 unigenes were assembled from combined reads of these libraries. A total of 32,475 unigenes were annotated by BLAST search to NCBI non-redundant protein (NR), Swiss-Prot, Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Of these, almost fifteen thousand unigenes were identified as significantly differentially expressed genes (DEGs) by using Reads Per kb per Million reads (RPKM) method. A total of 6,415 DEGs were mapped to 128 KEGG pathways, and 8,743 DEGs were assigned to 54 Gene Ontology categories. After blasting the DEGs to public sequence databases, 539 potential flowering-related DEGs were identified. In addition, 107 flowering-time genes were identified in longan, their expression levels between two longan samples were compared by RPKM method, of which the expression levels of 15 were confirmed by real-time quantitative PCR. Our results suggest longan homologues of SHORT VEGETATIVE PHASE (SVP), GIGANTEA (GI), F-BOX 1 (FKF1) and EARLY FLOWERING 4 (ELF4) may be involved this flowering trait and ELF4 may be a key gene. The identification of candidate genes related to continuous flowering will provide new insight into the molecular process of regulating flowering time in woody plants.

Show MeSH