Longan unigenes that share homology to flowering-time genes of other plants.

<p>Longan unigenes that share homology to flowering-time genes of other plants.</p

Summary of sequence assembling results after Illumina sequencing of cDNA libraries from ‘Sijimi’ and ‘Lidongben’ of longan.

<p>Summary of sequence assembling results after Illumina sequencing of cDNA libraries from ‘Sijimi’ and ‘Lidongben’ of longan.</p

Identification of Regulatory Genes Implicated in Continuous Flowering of Longan (<i>Dimocarpus longan</i> L.)

<div><p>Longan (<i>Dimocarpus longan</i> 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 <i>de novo</i> 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 <i>SHORT VEGETATIVE PHASE</i> (<i>SVP</i>), <i>GIGANTEA</i> (<i>GI</i>), <i>F-BOX 1</i> (<i>FKF1</i>) and <i>EARLY FLOWERING 4</i> (<i>ELF4</i>) may be involved this flowering trait and <i>ELF4</i> 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.</p></div

Differentially expressed genes between the ‘Lidongben’ and ‘Sijimi’.

<p>‘ALL DEGs’ indicates those unigenes showing differential expression between the two samples, ‘DEGs’ indicates those unigenes with FDR≤ 0.001 and |log2Ratio| ≥ 1. The numbers of genes up-regulated and down-regulated in the ‘Sijimi’ relative to ‘Lidongben’ are indicated above the blue or red bars, respectively.</p

The top 20 pathway assignments of DEGs based on KEGG.

<p>The x-axis indicates the number of DEGs in a category. The y-axis from bottom to top shows the top 20 pathways.</p

Length distribution of unigenes after <i>de novo</i> assembly using the reads from S, L and S&L libraries.

<p>Numbers in square brackets (e.g., [200, 300] and [1800, 3000]) indicate the range of unigene length, ‘>3000’indicates unigenes longer than 3,000 bp. Numbers in parentheses (e.g., (6, 165) and (22, 661)) indicate the total number of unigenes falling in this length range.</p

Real-time quantitative RT-PCR confirmation of the differentially expressed genes between ‘Lidongben’ and ‘Sijimi’.

<p>Relative transcript levels are calculated by real-time PCR with β-actin as the standard. Data are means ± SD of three separate measurements. Duncan’s multiple range test between two samples, ** P ≤0.01.</p

Summary of functional annotation of assembled unigenes.

<p>Summary of functional annotation of assembled unigenes.</p

Histogram representation of Gene Ontology classification of DEGs.

<p>GO categories, shown in the x-axis, are grouped into three main ontologies: biological process, cellular component and molecular function. The right y-axis indicates the number of genes in each category, while the left y-axis indicates the percentage of total genes in that category.</p

Sepecific flowering traits in ‘Sijimi’ longan.

<p><b>A</b>. ‘Sijimi’ longan blossoming continuously, both terminal and axillary shoots can differentiate into inflorescences, flowers and fruits can be observed on one tree at the same time. B. When the growth is inhibited, apical buds develop into pure inflorescences. <b>C</b>. Scions of ‘Sijimi’ and ‘Lidongben’ were grafted on different branches of one rootstock plant.</p