A chromosome-level reference genome of the wax gourd (Benincasa hispida)

Luo, Wenlong; Yan, Jun; Luo, Sushan; Liu, Wenrui; Xie, Dasen; Jiang, Biao

doi:10.1038/s41597-023-01986-7

Cited by 9 publications

(12 citation statements)

References 36 publications

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“…SNPs and Insertion/Deletion (InDel) were checked with the GATK algorithm. The filter conditions for obtaining SNP loci according to Luo et al [ 43 ]. The ANNOVAR software annotated the gene functions.…”

Section: Methodsmentioning

confidence: 99%

A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt

Gong,

Wang,

et al. 2023

Horticulture Research

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Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC2F1 generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H2O2, and O2-, activated SA and JA signaling-dependent ISR, and displayed immune activation against R. solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivars-driven probiotics to ameliorate plant diseases.

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Section: Methodsmentioning

confidence: 99%

A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt

Gong,

Wang,

et al. 2023

Horticulture Research

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“…pepo) MU-CU-16, have been sequenced. The genome sequence of the former and its two cultivars, i.e., B227 and pf3, were discovered in 2019 [93] and 2023 [94]. The first had a size of 913.0 Mb, making it one of the largest genomes in the Cucurbitaceae family, and pf3 had the largest described sequence amounting to 975.6 Mb.…”

Section: Cucurbits Genomes Complexity and Characterisationmentioning

confidence: 99%

From Sequencing to Genome Editing in Cucurbitaceae: Application of Modern Genomic Techniques to Enhance Plant Traits

Pawełkowicz,

Zieniuk,

Staszek

et al. 2024

Agriculture

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The availability of genome-sequencing and genome-editing techniques has increased the applicability of innovative solutions, opening up revolutionary prospects for developments in horticultural plant breeding. The Cucurbitaceae family is a group of plants of great importance in horticulture due to their high nutritional and economic value. These plants serve as important models for elucidating the principles of plant development and refining yield improvement strategies. While traditional breeding approaches have made significant contributions to the production of cucurbits, they have also been limited by the reduced genetic diversity and lower rates of variation inherent in these species. This comprehensive review summarises the latest developments in genome editing in cucurbits. It covers various aspects of enhancing plant traits to resist biotic stresses such as pathogenic fungi and viruses, as well as abiotic stresses such as adverse climate change, especially stresses caused by drought and salinity. This study focused on improvements in plant quality and on the optimisation of plant architecture, sex determination of flowers and fruit features. This review provides insights that may hold great promise for the future of horticultural crop improvement and serves as an important reference for the advancement of genome-sequencing and gene-editing technologies in cucurbits.

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“…The advantage of SMRT technology lies in the ultra-long sequences, which in principle correspond to the full length of transcript sequences subjected to sequencing. In recent days, SMRT sequencing has been widely used to enrich the reference genome in expression studies of plant species or cultivars without a complete reference genome 20 – 23 . SMRT sequencing is also widely used in studies of alternative splicing, sequence repeats, long noncoding RNA, fusion genes, and gene discovery 14 , 20 , 24 .…”

Section: Background and Summarymentioning

confidence: 99%

Single molecule real-time sequencing data sets of Hypericum perforatum L. plantlets and cell suspension cultures

Selvakesavan,

Nuc,

Kolarčik

et al. 2024

Sci Data

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Hypericum is a large genus that includes more than 500 species of pharmacological, ecological and conservation value. Although latest advances in sequencing technologies were extremely exploited for generating and assembling genomes of many living organisms, annotated whole genome sequence data is not publicly available for any of the Hypericum species so far. Bioavailability of secondary metabolites varies for different tissues and the data derived from different cultures will be a valuable tool for comparative studies. Here, we report the single molecule real-time sequencing (SMRT) data sets of Hypericum perforatum L. plantlets and cell suspension cultures for the first time. Sequencing data from cell suspension cultures yielded more than 33,000 high-quality transcripts from 20 Gb of raw data, while more than 55,000 high-quality transcripts were obtained from 35 Gb of raw data from plantlets. This dataset is a valuable tool for comparative transcriptomic analysis and will help to understand the unknown biosynthetic pathways of high medicinal value in the Hypericum genus.

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A chromosome-level reference genome of the wax gourd (Benincasa hispida)

Cited by 9 publications

References 36 publications

A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt

A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt

From Sequencing to Genome Editing in Cucurbitaceae: Application of Modern Genomic Techniques to Enhance Plant Traits

Single molecule real-time sequencing data sets of Hypericum perforatum L. plantlets and cell suspension cultures

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