A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

Deng, Yun; Liu, Shoucheng; Zhang, Yilin; Tan, Jingsheng; Li, Xiaopeng; Chu, Xiao; Xu, Baicheng; Tian, Yao; Sun, Yankuo; Li, Bosheng; Xu, Yunbi; Deng, Xing Wang; He, Hang; Zhang, Xingping

doi:10.1016/j.molp.2022.06.010

Cited by 116 publications

(76 citation statements)

References 83 publications

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“…2A . Using Tandem Repeats Finder (4.07b) [ 27 ], we identified centromeric sequences from the assembled genomes, and the most abundant tandem repeat is the centromere DNA [ 28 ]. Using the seven-base telomeric repeat (CCCTAAA at the 5′ end or TTTAGGG at the 3′ end) as a sequence query, we identified 18 telomeres.…”

Section: Resultsmentioning

confidence: 99%

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Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics

Zheng

Guo

et al. 2022

Horticulture Research

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Momordica charantia L. var. abbreviata Ser. (Mca), known as bitter gourd or bitter melon, is a Momordica variety with medicinal value and belongs to the Cucurbitaceae family. In view of the lack of genomic information on bitter gourd and other Momordica species and to promote Mca genomic research, we assembled a 295.6 Mb telomere-to-telomere (T2T) high-quality Mca genome with six gap-free chromosomes after Hi-C correction. This genome is anchored to 11 chromosomes, which is consistent with the karyotype information, and comprises 98 contigs (N50 of 25.4 Mb) and 95 scaffolds (N50 of 25.4 Mb). The Mca genome harbors 19,895 protein-coding genes, and 45.59% constitutes predicted repeat sequences. Synteny analysis revealed variations involved in fruit quality during the divergence of bitter gourd. In addition, assay for transposase-accessible chromatin (ATAC) by high-throughput sequencing and metabolic analysis showed that momordicosides and other substances are characteristic of Mca fruit pulp. A combined transcriptomic and metabolomic analysis revealed the mechanisms of pigment accumulation and cucurbitacin biosynthesis in Mca fruit peels, providing fundamental molecular information for further research on Mca fruit ripening. This report provides a new genetic resource for Momordica genomic studies and contributes additional insights into Cucurbitaceae phylogeny.

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Section: Resultsmentioning

confidence: 99%

“…In Cucurbitaceae species, Deng et al . [ 28 ] have assembled a gap-free watermelon genome of 11 chromosomes. These are fundamental for genome structure exploration and plant breeding as well as for trait selection.…”

Section: Discussionmentioning

confidence: 99%

Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics

Zheng

Guo

et al. 2022

Horticulture Research

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“…This is not just a milestone of human genomics, but also has a profound impact on animal and plant genomic research by kicking off an ambitious journey to resolve the complete genome sequence of all known living organisms on this planet. In fact, shortly after the publication of the human T2T genome assembly, the nearly complete genome sequence of A. thaliana [ 246 , 247 ], and the gap-free reference genomes of rice [ 248 ] and watermelon [ 249 ] were reported. The nearly complete genome sequences of plants reveal tandem repeats of satellite regions located in centromeres, and find new genes that weren’t accessible in previous versions of assemblies.…”

Section: Opportunities and Challenges For Future Pnp Researchmentioning

confidence: 99%

Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era

Guo¹,

Yao

Chen³

et al. 2022

Horticulture Research

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Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology and chemical informatics, are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.

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“…In bitter gourd, the functional study of genetics is considerably behind other Cucurbitaceae crops like watermelon and cucumber because of the lack of mutants ( Deng et al., 2022 ; Zhang et al., 2022 ). A long-recognized large-scale method for mutant acquisition is mutagenization using chemical or physical mutagens.…”

Section: Introductionmentioning

confidence: 99%

“…Because EMS mutagenesis is easy to control, exhibits a high mutation rate, and causes less harm to plants, it was widely used in rice ( Henry et al., 2014 ), maize ( Lu et al., 2018 ), soybean ( Li et al., 2017 ), pepper ( Arisha et al., 2015 ), cabbage ( Sun et al., 2022 ), watermelon ( Deng et al., 2022 ), cucumber ( Zhang et al., 2022 ) and Gossypium hirsutum L ( Lian et al., 2020 ). EMS concentrations differ from one crop to another, and a suitable mutagen concentration can be used to achieve the desired effect.…”

Section: Introductionmentioning

confidence: 99%

Construction of a density mutant collection in bitter gourd via new germplasms innovation and gene functional study

Wang

et al. 2022

Front. Plant Sci.

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Although a few studies have elucidated the creation of bitter gourd mutants, the suitable concentration and duration of ethyl methanesulfonate (EMS) mutagenesis have not been determined. In this study, mutant collection was conducted to create new germplasms and widen genetic diversity. By employing the seeds of the inbred line Y52 as the mutagenic material, EMS as the mutagen, and the suitable mutagenic conditions for bitter gourd seeds (EMS concentration 0.2%, mutagenic time 10 h), we mutated 10,000 seeds and acquired 3223 independent M1 lines. For the randomly selected 1000 M2 lines, 199 M2 lines with visible phenotypes were found, and 167 M2 lines were mutants of fruit shape, size, and tubercles. Furthermore, fourteen dwarf, eleven leaf color, five leaf shape, and eight meristem defect mutants were discovered in this mutant collection. In addition, three lines of 1253, 2284, and 3269 represented recessive mutants crossed with Y52. Furthermore, the yellow leaf lines of 2284 and 3269 were not mutated at the same gene locus. This study constructed a mutant collection through innovative new germplasms and provided valuable resources for bitter gourd breeding and functional gene research.

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A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

Cited by 116 publications

References 83 publications

Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics

Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics

Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era

Construction of a density mutant collection in bitter gourd via new germplasms innovation and gene functional study

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