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Characterization of the complete chloroplast genome of Dioscorea polystachya Turcz.

ABSTRACT: Dioscorea polystachya Turcz. is an important Chinese herbal medicine and the raw material of the medicine ingrediente (Chinese yam polysaccharide). It belongs to Dioscorea, which has 60 species and distribute in middle and southeast of China. In this study, we sequenced the sample of D. polystachya based on Jiaozuo, Henan and determined its complete chloroplast genome. The length of cp genome was 152,958 bp, includes two invert repeats (IR) regions of 25,492 bp, a large single-copy (LSC) region of 83,152 bp, and a short single-copy (SSC) region of 18,822 bp. There were 131 genes, which included 85 protein coding genes, 8 rRNA, and 38 tRNA, and overall GC content covered by 37.1%. Each of trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA genes contained an intron, clpP and ycf3 contained 2 introns. The phylogenetic position showed that D. Polystachya had the closest relationship with Dioscorea alata (MG267382) and Dioscorea aspersa (NC039807).

SUBMITTER: Hu N

PROVIDER: S-EPMC8143605 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Dioscorea is an important but underutilized genus of flowering plants that grows predominantly in tropical and subtropical regions. Several species, known as yam, develop large underground tubers and aerial bulbils that are used as food. The Chinese yam (D. polystachya Turcz.) is one of the few Dioscorea species that grows well in temperate regions and has been proposed as a climate-resilient crop to enhance food security in Europe. However, the fragile, club-like tubers are unsuitable for mechanical harvesting, which is facilitated by shorter and thicker storage organs. Brassinosteroids (BRs) play a key role in plant cell division, cell elongation and proliferation, as well as in the gravitropic response. We collected RNA-Seq data from the head, middle and tip of two tuber shape variants: F60 (long, thin) and F2000 (short, thick). Comparative transcriptome analysis of F60 vs. F2000 revealed 30,229 differentially expressed genes (DEGs), 1,393 of which were differentially expressed in the growing tip. Several DEGs are involved in steroid/BR biosynthesis or signaling, or may be regulated by BRs. The quantification of endogenous BRs revealed higher levels of castasterone (CS), 28-norCS, 28-homoCS and brassinolide in F2000 compared to F60 tubers. The highest BR levels were detected in the growing tip, and CS was the most abundant (439.6 ± 196.41 pmol/g in F2000 and 365.6 ± 112.78 pmol/g in F60). Exogenous 24-epi-brassinolide (epi-BL) treatment (20 nM) in an aeroponic system significantly increased the width-to-length ratio (0.045 ± 0.002) compared to the mock-treated plants (0.03 ± 0.002) after 7 weeks, indicating that exogenous epi-BL produces shorter and thicker tubers. In this study we demonstrate the role of BRs in D. polystachya tuber shape, providing insight into the role of plant hormones in yam storage organ development. We found that BRs can influence tuber shape in Chinese yam by regulating the expression of genes involved cell expansion. Our data can help to improve the efficiency of Chinese yam cultivation, which could provide an alternative food source and thus contribute to future food security in Europe.

Dataset Information

Characterization of the complete chloroplast genome of Dioscorea polystachya Turcz.

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