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Selenicereus monacanthus

ABSTRACT: Indentification of salt tolerant genes by RNA-Seq in red pitaya

PROVIDER: PRJDB6887 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR128251_1.fastq.gz	Fastqsanger.gz
	DRR128251_2.fastq.gz	Fastqsanger.gz
	DRR128252_1.fastq.gz	Fastqsanger.gz
	DRR128252_2.fastq.gz	Fastqsanger.gz
	DRR128253_1.fastq.gz	Fastqsanger.gz

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Transcriptomic de novo analysis of pitaya (Hylocereus polyrhizus) canker disease caused by Neoscytalidium dimidiatum

Project description:Canker disease caused by Neoscytalidium dimidiatum is the most serious disease that attacks the pitaya industry. One pathogenic fungus, referred to as ND8, was isolated from the wild-type red-fleshed pitaya (Hylocereus polyrhizus) of Hainan Province. Here, we studied mainly the host responses of red-fleshed pitaya (H. polyrhizus) cultivars against N. dimidiatum using Illumina RNA-Seq technology.

2019-01-17 | GSE119976 | GEO

Selenicereus monacanthus

Project description:Selenicereus monacanthus Raw sequence reads

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Project description:Selenicereus monacanthus Transcriptome or Gene expression

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Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications.

Project description:BackgroundMitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported.ResultsThis study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019 bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (≥ 50 bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437 bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523 bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3).ConclusionsThis study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.

| S-EPMC10625231 | biostudies-literature

The complete plastomes of red fleshed pitaya (<i>Selenicereus monacanthus</i>) and three related <i>Selenicereus</i> species: insights into gene losses, inverted repeat expansions and phylogenomic implications.

Project description:Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we have reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandifloras, and S. validus) and carried out a comprehensive comparative analysis. All four Selenicereus plastomes have a typical quartile structure. The plastome size ranged from 133,146 to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the inverted repeat regions had undergone a dramatic expansion and formed a previously unreported small single copy/inverted repeat border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Our study enriches the plastome in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-01121-z.

| S-EPMC8847515 | biostudies-literature

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