Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

Abstract

BackgroundLongan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting D. longan fruit yield, the difficulty and instability of blossoming is one of the most challenging issues. Perpetual flowering (PF) is a crucial trait for fruit trees and is directly linked to production potential. Therefore, studying the molecular regulatory mechanism of longan PF traits is crucial for understanding and solving problems related to flowering. In this study, comparative transcriptome analysis was performed using two longan cultivars that display opposite flowering phenotypes during floral induction.ResultsWe obtained 853.72 M clean reads comprising 125.08 Gb. After comparing these data with the longan genome, 27,266 known genes and 1913 new genes were detected. Significant differences in gene expression were observed between the two genotypes, with 6150 and 6202 differentially expressed genes (DEGs) for ‘SJ’ and ‘SX’, respectively. The transcriptional landscape of floral transition at the early stage was very different in these two longan genotypes with respect to key hormones, circadian rhythm, sugar metabolism, and transcription factors. Almost all flowering-related DEGs identified are involved in photoperiod and circadian clock pathways, such as CONSTANS-like (COL), two-component response regulator-like (APRRs), gigantea (GI), and early flowering (EFL). In addition, the leafy (LFY) gene, which is the central floral meristem identity gene, may inhibit PF formation in ‘SJ’.ConclusionThis study provides a platform for understanding the molecular mechanisms responsible for changes between PF and seasonal flowering (SF) longan genotypes and may benefit studies on PF trait mechanisms of evergreen fruit trees.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5461-3) contains supplementary material, which is available to authorized users.

Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Longan (Dimocarpus longan L.)

“…'Shixia' and 'Lidongben' are common longan varieties exhibiting seasonal flowering traits, while 'Sijimi' is a specific variety with continuous flowering trait. Firstly, the expression patterns of 17 DlARF genes were analyzed using RNA-seq databases of apical buds during floral bud development in 'Shixia' [33]. In Guangdong Province of China, apical buds in November are at the stage of before the emergence of floral primordia, apical buds in December are at the stage of floral organ differentiation which is characterized by the appearance of red dot, and apical buds in January is characterized by the appearance of the first inflorescence [33].…”

“…Firstly, the expression patterns of 17 DlARF genes were analyzed using RNA-seq databases of apical buds during floral bud development in 'Shixia' [33]. In Guangdong Province of China, apical buds in November are at the stage of before the emergence of floral primordia, apical buds in December are at the stage of floral organ differentiation which is characterized by the appearance of red dot, and apical buds in January is characterized by the appearance of the first inflorescence [33]. The results showed that there were nine DlARFs (DlARF-1,-2,-4,-6,-8,-9,-10,-11,-16) that showed higher transcript levels in November and December in 'Shixia' (Figure 6a).…”

“…Considering the significance of ARFs in plant growth and development, information on ARF gene family of longan is needed for better understanding. In this study, a comprehensive analysis of ARF family genes was conducted in longan based on its genomic sequence and three transcriptome databases [31][32][33]. A total 17 Dimocarpus longan ARF (DlARF) genes were identified and their physical and chemical properties, conserved motifs, genomic structures, evolutionary relationship and functional classification were analyzed.…”

Genome-Wide Identification and Expression Analysis of Sugar Transporter (ST) Gene Family in Longan (Dimocarpus longan L.)

“…The discovery the AS events of DlSTs, we use three transcriptome databases, including one for different longan varieties ('Sijimi' and 'Lidongben') [64], one for different floral bud development stages in 'Shixia' cultivar [65], and one 'Sijimi' transcriptome database containing nine longan tissues [59]. The quality of RNA-seq data are listed in Table S4.…”

Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions

“…Variety breeding has always been important for improving longan production, typically targeting two main traits, size and sweetness of the fruit 18, 19 . The breeding and extension of excellent varieties can enhance the stress resistance of fruit trees, improve the fruit quality and expand the planting area.…”