Dataset Information

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

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.

SUBMITTER: Jia T

PROVIDER: S-EPMC4257721 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Jia Tianqi T Wei Danfeng D Meng Shan S Allan Andrew C AC Zeng Lihui L

PloS one 20141205 12

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 ...[more]

PMID: 25479005

Similar Datasets

Project description:Longan (Dimocarpus longan Lour.) is a productive fruit crop with high nutritional and medical value in tropical and subtropical regions. The MYB gene family is one of the most widespread plant transcription factor (TF) families participating in the flowering regulation. However, little is known about the MYB TFs involved in the flowering process in longan and its regulatory network. In this study, a total of 119 DlR2R3-MYB genes were identified in the longan genome and were phylogenetically grouped into 28 subgroups. The groupings were supported by highly conserved gene structures and motif composition of DlR2R3-MYB genes in each subgroup. Collinearity analysis demonstrated that segmental replications played a more crucial role in the expansion of the DlR2R3-MYB gene family compared to tandem duplications, and all tandem/segmental duplication gene pairs have evolved under purifying selection. Interspecies synteny analysis among longan and five representative species implied the occurrence of gene duplication events was one of the reasons contributing to functional differentiation among species. RNA-seq data from various tissues showed DlR2R3-MYB genes displayed tissue-preferential expression patterns. The pathway of flower development was enriched with six DlR2R3-MYB genes. Cis-acting element prediction revealed the putative functions of DlR2R3-MYB genes were related to the plant development, phytohormones, and environmental stresses. Notably, the orthologous counterparts between Arabidopsis and longan R2R3-MYB members tended to play conserved roles in the flowering regulation and stress responses. Transcriptome profiling on off-season flower induction (FI) by KClO3 indicated two up-regulated and four down-regulated DlR2R3-MYB genes involved in the response to KClO3 treatment compared with control groups. Additionally, qRT-PCR confirmed certain genes exhibited high expression in flowers/flower buds. Subcellular localization experiments revealed that three predicted flowering-associated MYB proteins were localized in the nucleus. Future functional studies on these potential candidate genes involved in the flowering development could further the understanding of the flowering regulation mechanism.

Project description:Longan (Dimocarpus longan Lour.) is an important commercial fruit tree in southern China. The embryogenesis of longan affects the quality and yield of fruit. A large number of alternative splicing events occurs during somatic embryogenesis (SE), which is regulated by serine/arginine-rich (SR) proteins. However, the functions of SR proteins in longan are poorly understood. In this study, 21 Dlo-SR gene family members belonging to six subfamilies were identified, among which Dlo-RSZ20a, Dlo-SR30, Dlo-SR17, Dlo-SR53 and Dlo-SR32 were localized in the nucleus, Dlo-RSZ20b, Dlo-RSZ20c, Dlo-RSZ20d, Dlo-SC18, Dlo-RS2Z29, Dlo-SCL41, and Dlo-SR33 were localized in chloroplasts, and Dlo-RS43, Dlo-SC33, Dlo-SC37, Dlo-RS2Z33, Dlo-RS2Z16, Dlo-RS2Z24, Dlo-SCL43, Dlo-SR112, and Dlo-SR59 were localized in the nucleus and chloroplasts. The Dlo-SR genes exhibited differential expression patterns in different tissues of longan. The transcript levels of Dlo-RSZ20a, Dlo-SC18, Dlo-RS2Z29, DLo-SR59, Dlo-SR53, and Dlo-SR17 were low in all analyzed tissues, whereas Dlo-RS43, Dlo-RS2Z16, Dlo-RS2Z24, and Dlo-SR30 were highly expressed in all tissues. To clarify their function during SE, the transcript levels of Dlo-SR genes were analyzed at different four stages of SE, comprising non-embryonic callus (NEC), friable-embryogenic callus (EC), incomplete compact pro-embryogenic culture (ICpEC) and globular embryo (GE). Interestingly, the transcript levels of Dlo-RS2Z29 and Dlo-SR112 were increased in embryogenic cells compared with the NEC stage, whereas transcript levels of Dlo-RSZ20a, Dlo-RS43, Dlo-SC37, and Dlo-RS2Z16 were especially increased at the GE stage compared with the other stages. Alternative splicing events of Dlo-SR mRNA precursors (pre-mRNAs) was detected during SE, with totals of 41, 29, 35, and 44 events detected during NEC, EC, ICpEC, and GE respectively. Protein-protein interaction analysis showed that SR proteins were capable of interaction with each other. The results indicate that the alternative splicing of Dlo-SR pre-mRNAs occurs during SE and that Dlo-SR proteins may interact to regulate embryogenesis of longan.

Project description:Auxin response factor (ARF) is the key regulator involved in plant development. Despite their physiological importance identified in various woody plants, the functions of ARF genes in longan were still not clear. In this study, 17 longan ARF genes (DlARF) were identified using the reference longan genome data. According to the phylogenetic relationships among longan, Arabidopsis and apple, DlARFs were divided into four classes. Most DlARFs showed a closer relationship with ARFs from apple than those from Arabidopsis. The analysis of gene structure and domain revealed high similarity of different ARF genes in the same class. Typical features of B3-type DNA binding domain (DBD) motif, Auxin Resp motifs, and a highly conserved C-terminal Phox and Bem1 (PB1) domain were present in all DlARFs except for DlARF-2,-3,-13 which lacked PBI domain. Expression profiles of 17 DlARF genes in longan different tissues showed that some DlARF genes were tissues-specific genes. Analysis of three longan transcriptomes showed seven DlARFs (DlARF-1,-2,-6,-8,-9,-11,-16) had higher expression levels during floral bud differentiation of common longan and in the buds of 'Sijimi', suggesting these genes may promote floral bud differentiation in longan. Further qPCR analysis showed that among seven DlARF genes, the expression levels of DlARF-2,-6,-11,-16 increased significantly during the physiological differentiation stage of longan floral buds, confirming that they may play a role in flowering induction. Promoter sequence analysis revealed cis-elements related to flowering induction such as low-temperature responsiveness motif and circadian control motif. Motifs linked with hormone response for instance Auxin, MeJA, Gibberellin, and Abscisic acid were also found in promoters. This study provides a comprehensive overview of the ARF gene family in longan. Our findings could provide new insights into the complexity of the regulation of ARFs at the transcription level that may be useful to develop breeding strategies to improve development or promote flowering in longan.

Project description:GATA transcription factors, which are DNA-binding proteins with type IV zinc finger binding domains, have a role in transcriptional regulation in biological organisms. They have an indispensable role in the growth and development of plants, as well as in improvements in their ability to face various environmental stresses. To date, GATAs have been identified in many gene families, but the GATA gene in longan (Dimocarpus longan Lour) has not been studied in previous explorations. Various aspects of genes in the longan GATA family, including their identification and classification, the distribution of their positions on chromosomes, their exon/intron structures, a synteny analysis, their expression at different temperatures, concentration of PEG, early developmental stages of somatic embryos and their expression levels in different tissues, and concentrations of exogenous hormones, were investigated in this study. This study showed that the 22 DlGATAs could be divided into four subfamilies. There were 10 pairs of homologous GATA genes in the synteny analysis of DlGATA and AtGATA. Four segmental replication motifs and one pair of tandem duplication events were present among the DlGATA family members. The cis-acting elements located in promoter regions were also found to be enriched with light-responsive elements, which contained related hormone-responsive elements. In somatic embryos, DlGATA4 is upregulated for expression at the globular embryo (GE) stage. We also found that DlGATA expression was strongly up-regulated in roots and stems. The study demonstrated the expression of DlGATA under hormone (ABA and IAA) treatments in embryogenic callus of longan. Under ABA treatment, DlGATA4 was up-regulated and the other DlGATA genes did not respond significantly. Moreover, as demonstrated with qRT-PCR, the expression of DlGATA genes showed strong up-regulated expression levels under 100 μmol·L-1 concentration IAA treatment. This experiment further studied these and simulated their possible connections with a drought response mechanism, while correlating them with their expression under PEG treatment. Overall, this experiment explored the GATA genes and dug into their evolution, structure, function, and expression profile, thus providing more information for a more in-depth study of the characteristics of the GATA family of genes.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets