Comparative transcriptomic analysis of the regulation of flowering in temperate and tropical lotus (Nelumbo nucifera) by RNA‐Seq

Abstract

The switch from vegetative to reproductive growth is a major developmental transition in flowering plants, which depends on the balanced expression of the genes within a complex network that is controlled by both environmental and endogenous factors. Molecular regulation of flower development has been investigated extensively in model plants, particularly Arabidopsis. However, little is known about the mechanisms that regulate flowering in lotus. To analyse the molecular regulation of flowering in lotus, comparative transcript profiling was performed at two stages of bud development – the initial developmental stage (T1) and the fast developing stage (T2) – in the lotus cultivars ‘BG’ (B, temperate lotus) and ‘WR1’ (W, tropical lotus). A total of 140 504 368 high‐quality 100‐bp reads were obtained and aligned against the lotus reference genome. Of the 23 361 genes assembled, at least 88% of these transcripts were detected in each sample. These genes were significantly enriched in 40 Gene Ontology terms and 236 Kyoto Encyclopedia of Genes and Genomes pathways. Further comparisons of the transcripts in the four libraries revealed that 1808, 1330, 785, 702, 1954, and 2050 genes were differentially expressed between BT1 and BT2, WT1 and WT2, BT1 and WT1, BT2 and WT2, BT1 and WT2 and BT2 and WT1 samples, respectively. Analysis of the four libraries identified 147 lotus flowering‐time genes homologous to genes that control flowering‐time pathways in other plants. Differential regulation of the COP1, CCA1, LHY, CO‐LIKE, VIN3, GAI, and FT genes, which participate in the photoperiod, vernalization and gibberellic acid pathways, suggested that they might control the early flowering of lotus. The extensive transcriptome dataset should provide a foundation for comparative gene expression studies on the regulation of flowering in lotus. Comparative transcriptomic analysis detected several differentially expressed genes and potential candidate genes required for early flowering in lotus. These results provide new insight into the molecular mechanisms that regulate flowering in lotus.

Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

“…From morphological and biogeographical studies, Asian lotus can also be divided into two ecotypes—temperate type with enlarged and starch‐enriched rhizome, short period of florescence, and dormancy induced by short‐photoperiod; and tropical type with whip‐like and thin rhizome, long period of florescence, and dormancy partially induced by short‐photoperiod (Wang and Zhang , ). Comparative transcriptomic studies suggest extensive transcriptional divergence between these two ecotypes during leaf and rhizome development (Yang et al ; Yang et al ; Shi et al ). Because of these characters of the tropical lotus, it has been frequently used to improve the flower traits of the temperate lotus by hybridization.…”

Proteomic analysis of flowers at two developmental stages in Thermopsis turcica (Fabaceae)

“…The preferential expression of MADS-box genes in flowers of legumes suggested a similar regulatory network during flower development in legumes (Jung et al, 2012;Singh et al, 2013). Although several works have provided useful information for understanding the transcriptional regulation during flower development (Singh et al, 2013;Nakamura et al, 2014;Yang et al, 2014), only a few studies have been performed at the proteome level (Dafny-Yelin et al, 2005;Ahsan and Komatsu, 2009;Chen et al, 2016;Zhang et al, 2016). In our study, a proteomic approach was used to identify proteins that may have potential roles in regulatory networks.…”

RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera)

“…A total of 177,540 AS events were identified in the four data sets, and were distributed in 18,842 genes, which accounted for 64% of the total expressed genes [ 3 , 38 ]. The ratio is similar with those reported in Arabidopsis [ 29 ] and soybean [ 31 ], but much higher than that reported in rice [ 30 ].…”

“…Both ‘BG’ and ‘ZO’ are temperate cultivars with enlarged rhizomes. To the contrast, ‘WR1’ and ‘RL’ are tropical cultivars with thin rhizomes [ 38 ]. These four cultivars have been conserved as rhizome at Wuhan Botanical Garden of the Chinese Academy of Sciences (N30°32′44.02″, E114°24′52.18″), Hubei Province, China for many years.…”