Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.
The development of the medicinal plant Rehmannia glutinosa L. are severely declined when are replanted on the soil of the preceding crops being themselves. The biological basis of this so called "replanting disease" is unknown. Here, we have exploited the parallel sequencing capacity of both RNA-seq and DGE technology to ascertain what genes are responsive to the replanting disease in roots of R. glutinosa. RNA-seq analysis generated 99,708 non-redundant consensus sequences from the roots of the first year (R1) and the second year (R2) replanted R. glutinosa plants. From this set, a total of 48,616 transcripts containing a complete or partial encoding region was identified. Based on this resource, two DGE tag libraries were established to capture the transcriptome differences between the R1 and R2 libraries. Finally, a set of 2,817 (1,676 up- and 1,141 down-regulated) differentially transcribed genes was screened, and 114 most strongly differentially transcribed genes were identified by DGE analysis between first year and replanted plants. Furthermore, a more detailed examination of 16 selected candidates was carried out by qRT-PCR. The indication was that replanting could promote Ca(2+) signal transduction and ethylene synthesis, resulting in forming of the replanting disease. We analyzed the biomass indexes of replanted R. glutinosa roots by irrigating Ca(2+) signal blockers. The results suggested that the alleviation of the disease impairment could be the decrease of Ca(2+) signal transduction. This study provided a global survey of the root transcriptome in replanted R. glutinosa roots at the tuberous root expansion stage. As a result, a number of candidate genes underlying the replanting disease have been identified.
Alkaline/neutral invertase (NINV) proteins irreversibly cleave sucrose into fructose and glucose, and play important roles in carbohydrate metabolism and plant development. To investigate the role of NINVs in the development of pepper fruits, seven NINV genes (CaNINV1–7) were identified. Phylogenetic analysis revealed that the CaNINV family could be divided into α and β groups. CaNINV1–6 had typical conserved regions and similar protein structures to the NINVs of other plants, while CaNINV7 lacked amino acid sequences at the C-terminus and N-terminus ends. An expression analysis of the CaNINV genes in different tissues demonstrated that CaNINV5 is the dominant NINV in all the examined tissues (root, stem, leaf, bud, flower, and developmental pepper fruits stage). Notably, the expression of CaNINV5 was found to gradually increase at the pre-breaker stages, followed by a decrease at the breaker stages, while it maintained a low level at the post-breaker stages. Furthermore, the invertase activity of CaNINV5 was identified by functional complementation of the invertase-deficient yeast strain SEY2102, and the optimum pH of CaNINV5 was found to be ~7.5. The gene expression and enzymatic activity of CaNINV5 suggest that it might be the main NINV enzyme for hydrolysis of sucrose during pepper fruit development.
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