- Significant differences in gene expression were observed between the two genotypes, with 6150 and 6202 differentially expressed genes (DEGs) for ‘ SJ ’ and ‘ SX. - during the floral induction process was performed using two longan cultivars (‘SJ’ and ‘SX. - longan ‘SJ’ and ‘SX’ (nine-year-old trees), which dis- play opposite flowering phenotypes, were grown at an experimental orchard of the South Subtropical Crops Research Institute of the Chinese Academy of Tropical Agricultural Science in Zhanjiang, China (110°16′ E, 21°. - Three different types of ‘SJ’ and ‘SX’ apical buds were used in this study. - To detect transcriptional changes in ‘SJ’ and. - To evaluate gene expression patterns during floral induction in ‘SJ’ and ‘SX. - expression pattern analyses were per- formed, and DEGs for ‘SJ’ and ‘SX’ were clustered into eight expression profiles using Short Time-series Expres- sion Miner (STEM) version 1.3.8 [29]. - To identify genetic differences that may contribute to the PF traits of ‘SJ’ at the transcriptional level, compara- tive transcript profiling of ‘SX’ and ‘SJ’ flower buds from three different developmental stages was performed using RNA-Seq. - Identification of DEGs between ‘ SJ ’ and ‘ SX ’ during floral induction. - DEGs were first identified through comparisons of the RPKM values for each gene of ‘SJ’ and ‘SX’ at different floral induction stages (SXT1-vs-SJT1, SXT2-vs-SJT2, and SXT3-vs-SJT3) with |log 2 Ratio. - Regarding DEGs between ‘SJ’ and ‘SX’ at the dormant stage (T1), GO terms related to “cytoskeletal” and. - “microtubule-based process” and “oxidation-reduction. - related to “binding” and “catalytic activity” in the mo- lecular function category were significantly enriched. - tin binding”, “actin binding”, and “hexokinase activity”, were found. - 1 Different flowering phenotypes and number of differentially expressed genes during floral induction in ‘ SJ ’ and ‘ SX ’ longan. - a Different flowering traits of ‘ SJ ’ and ‘ SX. - SJ ’ longan blossoms continuously. - b Venn diagram showing the number of DEGs between ‘ SJ ’ and ‘ SX ’ longan during the floral induction process. - c Venn diagram showing the number of DEGs during floral induction in ‘ SJ. - d Venn diagram showing the number of DEGs during floral induction in ‘ SX. - For the DEG comparison between ‘SJ’ and ‘SX’ at T2, pathways of “plant-pathogen interaction” (corrected q-value genes), “plant hormone signal trans- duction” (corrected q-value genes), and “cir- cadian rhythm-plant” (corrected q-value genes) were significantly enriched. - Finally, “plant hor- mone signal transduction” (corrected q-value genes) and “plant-pathogen interaction” (corrected q-value genes) were significantly enriched DEGs between ‘SJ’ and ‘SX’ at the T3 stage.. - The results of GO and KEGG enrichment analyses suggested that the DEGs between ‘SJ’ and ‘SX’ at the dormant stage (T1) are mainly related to genes involved in plant basal metabolic processes. - DEGs between ‘SJ’. - Quantitative transcriptomic changes during flower induction in ‘ SJ ’ and ‘ SX. - Gene expression over the developmental course of flower induction was comparatively examined (T1-vs- T2, T2-vs-T3, and T1-vs-T3), revealing that 6150 and 6202 DEGs were significantly expressed in ‘SJ’ and ‘SX. - To evaluate the expression profiles, trend analyses were performed using STEM software, and the DEGs in ‘SJ’ and. - In ‘SJ. - “photosynthesis”, “oxidation-reduction”, and “ATP/ADP. - (q-value genes), “benzoxazinoid biosyn- thesis” (q-value genes), and “plant hor- mone signal transduction” (q-value genes) were significantly enriched. - In ‘SX. - Compared to ‘SJ. - in ‘SX’. - “plant hormone signal transduction” (q-value genes), “limonene and pinene degradation” (q-value genes), and “diterpenoid biosynthesis”. - DEGs involved in “photosynthesis” and “regulation of biosynthetic process” were significantly enriched in profile 3, as were path- ways of “diterpenoid biosynthesis” (q-value . - genes), “photosynthesis” (q-value genes), “cir- cadian rhythm” (q-value genes) and “plant hormone signal transduction” (q-value genes). - 2 Trend analysis of DEGs with significant changes in expression profiles and KEGG pathway enrichment analysis for ‘ SJ ’ (a) and ‘ SX ’ (b). - (q-value genes), “linoleic acid metabol- ism” (q-value genes), and “cysteine and methionine metabolism” (q-value genes) were enriched in this profile. - “single-organism process” and cell wall association func-. - “ascorbate and aldarate metabolism” (q-value genes), “pyruvate metabolism” (q-value genes), and “riboflavin metabolism” (q-value genes) (Tables S8 and S9).. - Furthermore, the path- way related to photosynthesis clustered in different pro- files in ‘SJ’ and ‘SX. - As the starch and sucrose metabolism pathway was only significantly enriched in profile 6 in ‘SJ’ and the SXT1-vs-SJT1 comparison, the 97 DEGs (Additional file 11) in this pathway were further analyzed. - 33 genes were significantly upregulated during the T1 to T2 transition in ‘SJ. - No genes in ‘SJ’ were significantly up- or downregulated during the T2 to T3 transition. - and ‘SX’ and in different profiles in the two cultivars during floral induction. - DEGs related to hormone signaling pathways in ‘SJ’. - Three TGA TFs related to the SA pathway displayed downregula- tion in ‘SJ’ during T1 to T2. - most DEGs related to hormone biosynthesis and signaling path- ways in ‘SX’ were enriched in the late floral induction stage:. - In contrast, 92 DEGs displayed upregulation or down- regulation in ‘SX’ through T2 to T3 compared to ‘SJ’.. - The remaining genes were significantly and differentially expressed during T2 to T3 in ‘SX. - 3 Expression profiles of sugar-related genes and qRT-PCR identification of sugar-related gene expression levels in flower buds during the floral induction process in ‘ SJ ’ and ‘ SX ’ longan. - yet it showed no apparent change during the flower induction process in ‘SJ’. - 6, 19 GRAS TFs displayed differential expression during flower induction in ‘SJ’ and ‘SX. - including eight genes that were significantly up- or downregulated during T1 to T2 in ‘SJ’ and ten with differential expression during flower induction in ‘SX’. - eight genes that displayed differential expression during flower induc- tion in ‘SX. - Thirty-one NAC-like family members displayed differential expression during flower induction in ‘SJ’ and ‘SX. - 003709.1 and Dlo_005892.1) significantly downregu- lated genes during T1 to T2 in ‘SJ. - the remaining 19 genes displayed differential expression during flower induction in ‘SX’ (Additional file 14).. - Moreover, MYB family genes displayed differential ex- pression during flower induction in ‘SJ’ and ‘SX. - includ- ing 19 and eight with significant downregulation during T1 to T2 in ‘SJ. - 17 with differential expression during flower induction in ‘SX. - 4 Expression profiles of hormone-related genes and qRT-PCR identification of hormone-related gene expression levels in flower buds during the floral induction process in ‘ SJ ’ and ‘ SX ’ longan. - To further validate the RNA-Seq results, 38 DEGs in- volved in sugar metabolism, hormone signal transduction, photoperiod and circadian clock pathways were selected for parallel qRT-PCR-based expression analysis in ‘SJ’ and. - in these two longan cultivars (‘SJ’ and ‘SX’) during the floral induction process, DEGs were compared between these cultivars during flower induction. - A total of 6150 DEGs were identified during the floral induction process in ‘SJ. - in ‘SX. - 5 Expression profiles of flower-related genes and qRT-PCR identification of flower-related gene expression levels in flower buds during the floral induction process in ‘ SJ ’ and ‘ SX ’ longan. - 6 Expression profiles of transcription factor-related genes and qRT-PCR identification of transcription factor-related gene expression levels in flower buds during the floral induction process in ‘ SJ ’ and ‘ SX ’ longan. - In con- trast, almost all starch and sucrose-related DEGs in ‘SX’. - However, in this study, TPS1 was only sig- nificantly downregulated in ‘SJ. - Similarly, GBSS1, SS2, and pgm were also only downregulated in ‘SJ’.. - indole acetic acid (IAA) and zeatin ribosides (ZRs) differ during the natural floral differentiation process in ‘SJ’ and that ethephon and GA 3 may promote flower formation and fruit setting in. - ‘SJ’ longan [54]. - indicating these genes may participate in regulating floral induction in ‘SJ’.. - In this study, 7 gibberellin receptor GID1 and 4 DELLA genes were up- regulated in the early floral induction stage in ‘SJ. - induction stage in ‘SX. - In contrast, PYL genes were significantly upregulated but PP2C downregulated during the floral transition in ‘SJ’ and ‘SX. - Similarly, BSK (Dlo BZR1 (Dlo CYCD3 (Dlo_000396.1 and Dlo_011212.2) and most BRI1-like genes were upregulated in the early floral induction stage in ‘SJ’ (Fig. - Consistent with this result, levels of several BRI1-like genes decreased in the early floral induction stage in ‘SJ’.. - and ERF-1 (ethylene response factor) and TGA1 TF genes were downregu- lated during early floral induction in both ‘SJ’ and ‘SX’.. - In this study, 39 flower-related genes differentially expressed during floral induction between ‘SJ’ and ‘SX’ were identified (Fig. - COL10, Dlo_013961.1) were upregulated during the floral induc- tion process in ‘SJ. - TCP5-like, Dlo which act as CO activators [96], and the GAI gene were upregulated during floral induction in ‘SJ’.. - ‘SJ’ compared with ‘Lidongben. - Similarly, the EFL4-like gene (Dlo_027544.1) functions as a suppressor of floral induction in ‘SJ’. - APETALA2 (AP2), a target of miR172 that has been implicated in floral stem cell control [99], was downregulated during floral induc- tion in ‘SX. - though it showed no apparent changes during flower induction in ‘SJ. - In our study, 52 GRAS genes were found in the longan genome, and 19 GRAS TFs displayed differential expression during flower induction in ‘SJ’ and ‘SX’ (Fig. - Among them, 15 of these genes displayed dif- ferential expression during flower induction in ‘SJ’ and. - NAC participates in floral induction in several species and in longan, 31 of 107 NAC-like family members were differentially regu- lated during flower induction in ‘SJ’ and ‘SX’ (Fig. - Seven genes (Dlo_028054.1, Dlo_012365.1, Dlo_022129.1, Dlo_012309.3, Dlo_028436.1, Dlo_020074.1 and Dlo_005893.1) were common, and expression of the remaining genes was significantly altered during flower in- duction in ‘SJ’ and ‘SX’. - and 17 genes displayed differential expression dur- ing flower induction in ‘SX’ (Fig. - In addition, the LFY gene may inhibit PF in ‘SJ’ longan, though further analyses are required. - Additional file 4: DEGs between ‘ SJ ’ and ‘ SX ’ during floral induction.. - Additional file 5: Significantly enriched GO term analysis of DEGs between ‘ SJ ’ and ‘ SX ’ during floral induction. - Additional file 6: Significantly enriched KEGG pathway analysis of DEGs between ‘ SJ ’ and ‘ SX ’ during floral induction. - Additional file 7: DEGs in ‘ SJ ’ during floral induction. - (XLS 7620 kb) Additional file 8: DEGs in ‘ SX ’ during floral induction. - (XLS 7771 kb) Additional file 9: GO terms significantly overrepresented in the eight enriched profiles of gene expression versus the reference set in ‘ SJ ’ and. - Additional file 10: KEGG pathways significantly overrepresented in the eight enriched profiles of gene expression versus the reference set in ‘ SJ ’ and ‘ SX. - Old Blush ’ and R
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