Abstract
Watermelon is a highly important vegetable crop species worldwide, with its abundance of genetic resources aiding in identifying mechanisms and markers for molecular breeding. Typically diploid (2n = 2 × = 22), watermelon can also exhibit autopolyploidy, resulting in triploid (3n = 33) and tetraploid varieties (4n = 44). The whole genome sequence of numerous major species in this crop has been completed and is currently being utilized by researchers globally for GWAS and other investigations. Developing a pan-genome for watermelon using modern genomics technologies and enhancing the existing reference genome could greatly assist watermelon researchers and breeders.
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References
Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218
Bayer PE, Golicz AA, Scheben A, Batley J, Edwards D (2020) Plant pan-genomes are the new reference. Nat Plants 6:914–920
Chen N (2004) Using Repeat Marker to identify repetitive elements in genomic sequences. Curr Protoc Bioinf 5:4.10.1–4.10.14
Garcia-Lozano M, Natarajan P, Levi A, Katam R, Lopez-Ortiz C, Nimmakayala P, Reddy UK (2021) Altered chromat in conformation and transcriptional regulation in watermelon following genome doubling. Plant J 106:588–600
Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L, Ren Y, Wang Z (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58
Guo S, Zhao S, Sun H, Wang X, Wu S, Lin T, Ren Y, Gao L, Deng Y, Zhang J (2019) Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nat Genet 51:1616–1623
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272
Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z (2019) A chromosome-scale genome assembly of cucumber (Cucumis sativus L.) GigaSci 8:giz072
Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and glimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20:2878–2879
Ren Y, Mcgregor C, Zhang Y, Gong G, Zhang H, Guo S, Sun H, Cai W, Zhang J, Xu Y (2014) An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus). BMC Plant Biol 14:1–11
Renner SS, Wu S, Pérez-Escobar OA, Silber MV, Fei Z, Chomicki G (2021) A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Proc Natl Acad Sci 118:e2101486118
Stanke M and Waack S (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinf 19:ii215–ii225
Sun H, Wu S, Zhang G, Jiao C, Guo S, Ren Y, Zhang J, Zhang H, Gong G, Jia Z (2017) Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes. Mol Plant 10:1293–1306
Sun Y, Wang J, Li Y, Wang X, Xu WH, Wang YQ, Zhang PT, Zhang Y, Kong XD (2022) Pangenome analysis reveals the abundant gene presence/absence variations (PAVs) among different varieties of melon and their influence on traits. Front Plant Sci 420
Wang B, Yang X, Jia Y, Xu Y, Jia P, Dang N, Wang S, Xu T, Zhao X, Gao S (2021) High-quality Arabidopsis thaliana genome assembly with nanopore and HiFi long reads. Genomics, Proteomics Bioinf
Wu S, Shamimuzzaman M, Sun H, Salse J, Sui X, Wilder A, Wu Z, Levi A, Xu Y, Ling KS (2017) The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus. Plant J 92:963–975
Yao W, Li G, Zhao H, Wang G, Lian X, Xie W (2015) Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol 16:1–20
Zhang N, Bao Y, Xie Z, Huang X, Sun Y, Feng G, Zeng H, Ren J, Li Y, Xiong J (2019) Efficient Characterization of Tetraploid Watermelon. Plants 8:419
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Natarajan, P., Nimmakayala, P., Dutta, S.K., Reddy, U.K. (2023). Caveats for Watermelon Whole Genome Sequencing. In: Dutta, S.K., Nimmakayala, P., Reddy, U.K. (eds) The Watermelon Genome . Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-031-34716-0_2
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DOI: https://doi.org/10.1007/978-3-031-34716-0_2
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