The Ubiquitin-Conjugating Enzyme Gene Family in Longan (Dimocarpus longan Lour.): Genome-Wide Identification and Gene Expression during Flower Induction and Abiotic Stress Responses

Abstract

Ubiquitin-conjugating enzymes (E2s or UBC enzymes) play vital roles in plant development and combat various biotic and abiotic stresses. Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical region of Southeast Asia and Australia; however the characteristics of the UBC gene family in longan remain unknown. In this study, 40 D. longan UBC genes (DlUBCs), which were classified into 15 groups, were identified in the longan genome. An RNA-seq based analysis showed that DlUBCs showed distinct expression in nine longan tissues. Genome-wide RNA-seq and qRT-PCR based gene expression analysis revealed that 11 DlUBCs were up- or down-regualted in the cultivar “Sijimi” (SJ), suggesting that these genes may be important for flower induction. Finally, qRT-PCR analysis showed that the mRNA levels of 13 DlUBCs under SA (salicylic acid) treatment, seven under methyl jasmonate (MeJA) treatment, 27 under heat treatment, and 16 under cold treatment were up- or down-regulated, respectively. These results indicated that the DlUBCs may play important roles in responses to abiotic stresses. Taken together, our results provide a comprehensive insight into the organization, phylogeny, and expression patterns of the longan UBC genes, and therefore contribute to the greater understanding of their biological roles in longan.

The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System

“…20 E2 enzymes have been found in Caenorhabditis elegans [77], 40 in A. thaliana [68], 14 in Saccharomyces cerevisiae [78], 37 in human [67], 48 in rice [79], 75 in maize [80], 72 in banana [81], 43 in Vitis vinifera [82], 34 in Carica papaya [83], 59 in tomato [84], 40 in Dimocarpus longan Lour. [85], and 57 in potato [86].…”

“…in Vitis vinifera [82], 34 in Carica papaya [83], 59 in tomato [84], 40 in Dimocarpus longan Lour. [85], and 57 in potato [86]. The ubiquitin E2 variant (UEV) is similar to the E2 enzyme in both sequence and structure, but it cannot form a thioester linkage with ubiquitin because of the lack of the catalytic cysteine residue [87,88].…”

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

“…A total of 42 DlST genes underwent AS events in flower buds, with 38 genes in flower and 33 genes in pericarp, stem and young fruit; the AS events in pulp was the lowest (21) (Figure 7 and Table S2). By analyzing the transcriptome of nine tissues in 'Sijimi', we found that young fruit (143) and pulp (58) accounted for the largest and smallest number of AS events in DlST genes, respectively. Alternative 5 splice site (143) and skipped exon (58) was the most and least common, respectively.…”

“…By analyzing the transcriptome of nine tissues in 'Sijimi', we found that young fruit (143) and pulp (58) accounted for the largest and smallest number of AS events in DlST genes, respectively. Alternative 5 splice site (143) and skipped exon (58) was the most and least common, respectively. A total of 42 DlST genes underwent AS events in flower buds, with 38 genes in flower and 33 genes in pericarp, stem and young fruit; the AS events in pulp was the lowest (21) (Figure 7 and Table S2).…”

“…One microgram of purified RNA was reverse transcribed into cDNA using TransScript One-Step gDNA Removal and cDNA Synthesis SuperMix (TRANS, Beijing, China) following the manufacturer's protocol. qRT-PCR was performed using SYBR Green I Master Mix (Takara, Dalian, China) and the expression levels of ST genes were normalized to the longan Actin1 gene (Dlo_028674) [58]. qRT-PCR was performed on a LightCycler 96 Real-Time PCR Systems (Roche, NC, USA).…”