Fig 1.
Time course of adventitious root development in mung bean hypocotyls after the primary roots excision.
Adventitious root primordia are visible at 48 h after the primary roots excision and adventitious roots grow through the epidermis of the hypocotyls within 96 h. The basal 0.5 cm of hypocotyls at 0 h (Con), 6 h (Wat6), and 24 h (Wat24) after the primary roots excision and incubation in water were harvested and used as study samples.
Table 1.
Sequencing data information.
Table 2.
Statistics of reads assembly with the Trinity method.
Table 3.
Sample mapping results and unigene abundance measurements in the samples.
Fig 2.
Gene Ontology classification of mung bean transcriptome.
Unigenes with BLASTx matches against the plant Nr database were classified into three main GO categories (biological process, cellular component, molecular function) and 57 sub-categories. The left-hand scale on the y-axis shows the percentage of the unigenes in each of the categories. The right-hand scale on the y-axis indicates the number of the unigenes in the same category.
Fig 3.
KOG functional classification of the unigenes.
Unigenes were assigned to one or more of the 25 COG classification categories.
Fig 4.
Pathway annotation of the unigenes.
Table 4.
E-value distribution of the BLASTx hits against the Nr and TrEMBL databases for each unigene.
Table 5.
The top 10 pathways with highest percentages of unigenes mapped to.
Fig 5.
GO enrichment for up- and down-regulated unigenes.
Table 6.
Differentially enriched GO categories and KEGG pathways at the time points during adventitious rooting.
Table 7.
Top 10 significantly down- and up-regulated GO categories in the samples.
Table 8.
The pathway enrichment of the DEGs (FDR<0.05).
Table 9.
Top significantly up- and down-regulated KOs (p <0.01) in the three samples.
Table 10.
Statistics of the DEGs (FDR<0.001) at the time points during adventitious rooting in mung bean.
Table 11.
Top up-and down-regulated DEGs in the Wat6 sample.
Table 12.
Top up- and down-regulated DEGs in the Wat24 sample.
Table 13.
Top up- and down-regulated DEGs between Wat24 and Wat6 sample.
Fig 6.
Validation of selected genes involved in adventitious rooting by qRT-PCR.
The gene expression levels measured by qRT-PCR were compared with that of RNA-Seq. White histograms represent expression levels determined by RNA-Seq in RPKM units (left axis), while grey columns represent gene expression levels determined by qRT-PCR and normalized to three control genes (right axis). Bars represent the mean (± SE) of three experiments. Different letters (a, b, and c) represent statistically significant differences (P < 0.01) among the data of qRT-PCR, analysed using Student’s t-test.
Table 14.
Summary of the most differentially expressed genes during early stage of adventitious rooting in several plants investigated.