Population genomic analysis reveals genomic variations associated with domestication and key agronomic traits in bitter gourd (<i>Momordica charantia</i>)

Yu Niu; Rui Wang; Liang Wang; Aizheng Huang; Xu Han; Renbo Yu; Shijun Chen; Juntao Wang; Jiaowen Cheng; Changming Chen; Chengjie Chen; Yan Yang; Yi Liao; Ming Hu

doi:10.1016/j.jgg.2026.04.017

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2026 > Accepted Manuscript

PDF( 20529 KB)

Population genomic analysis reveals genomic variations associated with domestication and key agronomic traits in bitter gourd (Momordica charantia)

doi: 10.1016/j.jgg.2026.04.017

a. Tropical Crops Genetic Resources Research Institute, National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Science, Haikou 571101, Sanya 572024, Hainan, China;
b. Institute of Facility Agriculture of Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China;
c. Ministry of Agriculture and Rural Affairs Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China;
d. Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, Guangdong, China;
e. National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Science, Sanya 572024, Haikou 571101, Hainan, China

Funds:

This work was supported by the Hainan Province Science and Technology Special Fund (ZDYF2024XDNY183), the Project of National Key Laboratory for Tropical Crop Breeding (NKLTCBCXTD35), and the National Natural Science Foundation of China (32460760).

Received Date: 2025-12-18
Accepted Date: 2026-04-24
Rev Recd Date: 2026-04-22

Available Online: 2026-05-13

Abstract

Abstract

Bitter gourd (Momordica charantia) is a widely cultivated vegetable and medicinal crop for its nutritional and pharmaceutical properties. Yet, the genomic basis of its domestication and key agronomic traits remains largely unexplored. Here, we present a high-quality, chromosome-level genome assembly specifically representing a smooth bitter gourd cultivar (Y1745), with a total assembly size of 327.14 Mb, a contig N50 of 11.33 Mb, and a scaffold N50 of 23.47 Mb. Comparative genomics reveals lineage-specific expansions of gene families related to stress responses and secondary metabolism. Population genomic analysis of 192 globally representative accessions identifies three distinct genetic groups (China, Southeast Asia, and South Asia Subcontinent), reflecting complex demographic histories, and uncovers strong signatures of selection associated with domestication and regional adaptation. In the genome-wide association study (GWAS) of 35 traits, we identify 893 significant trait-associated loci. Notably, two candidate genes (McWRKY and McFPF1-like 1) are associated with flowering time regulation, and one candidate gene (McEXLB1) with fruit size determination. Our work provides valuable genomic resources for understanding bitter gourd domestication and offers potential genetic targets for breeding.
- Bitter gourd,
- Genome assembly,
- Population genomics,
- Domestication,
- Agronomic traits

FullText(HTML)

References(107)

References

Alexander, D.H., Novembre, J., Lange, K., 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655-1664.

Amirthaveni, M., Gomathi, K., Yang, R.-Y., 2018. Hypoglycemic effect of bitter gourd (Momordica charantia L) among pre diabetics in India: a randomized placebo controlled cross over study. Indian J. Nutr. Diet. 55, 44.

Andres, F., Coupland, G., 2012. The genetic basis of flowering responses to seasonal cues. Nat. Rev. Genet. 13, 627-639.

Barrera-Redondo, J., Sanchez-de la Vega, G., Aguirre-Liguori, J.A., Castellanos-Morales, G., Gutierrez-Guerrero, Y.T., Aguirre-Dugua, X., Aguirre-Planter, E., Tenaillon, M.I., Lira-Saade, R., Eguiarte, L.E., 2021. The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative. Hortic. Res. 8, 109.

Behera, T.K., Behera, S., Bharathi, L.K., John, K.J., Simon, P.W., Staub, J.E., 2010. Bitter gourd: botany, horticulture, breeding, in: Janick J. (ed.), Horticultural Reviews, Vol. 37. Wiley, pp. 101-141.

Browning, B.L., Tian, X., Zhou, Y., Browning, S.R., 2021. Fast two-stage phasing of large-scale sequence data. Am. J. Hum. Genet. 108, 1880-1890.

Cai, Y., Chen, X., Xie, K., Xing, Q., Wu, Y., Li, J., Du, C., Sun, Z., Guo, Z., 2014. Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice. PLOS ONE 9, e102529.

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L., 2009. BLAST+: architecture and applications. BMC Bioinform. 10, 421.

Campbell, M.S., Law, M., Holt, C., Stein, J.C., Moghe, G.D., Hufnagel, D.E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C.J., et al., 2013. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 164, 513-524.

Cantalapiedra, C.P., Hernandez-Plaza, A., Letunic, I., Bork, P., Huerta-Cepas, J., 2021. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825-5829.

Charrad, M., Ghazzali, N., Boiteau, V., Niknafs, A., 2014. NbClust: an R package for determining the relevant number of clusters in a data set. J. Stat. Softw. 61, 1-36.

Chen, H., Patterson, N., Reich, D., 2010. Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402.

Chen, S., Zhou, Y., Chen, Y., Gu, J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890.

Chen, X., Li, C., Wang, H., Guo, Z., 2019. WRKY transcription factors: evolution, binding, and action. Phytopathol. Res. 1, 13.

Cheng, H., Asri, M., Lucas, J., Koren, S., Li, H., 2024. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat. Methods 21, 967-970.

Chomicki, G., Schaefer, H., Renner, S.S., 2020. Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology. New Phytol. 226, 1240-1255.

Cosgrove, D.J., 2000. Loosening of plant cell walls by expansins. Nature 407, 321-326.

Cosgrove, D.J., 2015. Plant expansins: diversity and interactions with plant cell walls. Curr. Opin. Plant Biol. 25, 162-172.

Cui, J., Yang, Y., Luo, S., Wang, L., Huang, R., Wen, Q., Han, X., Miao, N., Cheng, J., Liu, Z., et al., 2020. Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.). Hortic. Res. 7, 85.

Cui, J., Zhou, Y., Zhong, J., Feng, C., Hong, Y., Hu, K., Cao, Y., 2022. Genetic diversity among a collection of bitter gourd (Momordica charantia L.) cultivars. Genet. Resour. Crop Evol. 69, 729-735.

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al., 2011. The variant call format and VCFtools. Bioinformatics 27, 2156-2158.

Danecek, P., McCarthy, S.A., 2017. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics 33, 2037-2039.

Dong, S.-S., He, W.-M., Ji, J.-J., Zhang, C., Guo, Y., Yang, T.-L., 2020. LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. Brief. Bioinform. 22, bbaa227.

Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., et al., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92-95.

Emms, D.M., Kelly, S., 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238.

Fu, A., Wang, Q., Mu, J., Ma, L., Wen, C., Zhao, X., Gao, L., Li, J., Shi, K., Wang, Y., et al., 2021. Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development. Hortic. Res. 8, 35.

Fu, A., Zheng, Y., Guo, J., Grierson, D., Zhao, X., Wen, C., Liu, Y., Li, J., Zhang, X., Yu, Y., et al., 2022. Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics. Hortic. Res. 10, uhac228.

Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, G., Gonzalez, V.M., Henaff, E., Camara, F., Cozzuto, L., Lowy, E., et al., 2012. The genome of melon (Cucumis melo L.). Proc. Natl. Acad. Sci. U. S. A. 109, 11872-11877.

Guo, J., Xu, W., Hu, Y., Huang, J., Zhao, Y., Zhang, L., Huang, C.-H., Ma, H., 2020. Phylotranscriptomics in Cucurbitaceae reveal multiple whole-genome duplications and key morphological and molecular innovations. Mol. Plant 13, 1117-1133.

Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., et al., 2013. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat. Genet. 45, 51-58.

Hackbusch, J., Richter, K., Muller, J., Salamini, F., Uhrig, J.F., 2005. A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins. Proc. Natl. Acad. Sci. U. S. A. 102, 4908-4912.

Han, M.V., Thomas, G.W.C., Lugo-Martinez, J., Hahn, M.W., 2013. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol. Biol. Evol. 30, 1987-1997.

Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W.J., Wang, X., Xie, B., Ni, P., et al., 2009. The genome of the cucumber, Cucumis sativus L. Nat. Genet. 41, 1275-1281.

Huang, X., Kurata, N., Wei, X., Wang, Z.-X., Wang, A., Zhao, Q., Zhao, Y., Liu, K., Lu, H., Li, W., et al., 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497-501.

Hufford, M.B., Xu, X., van Heerwaarden, J., Pyhajarvi, T., Chia, J.M., Cartwright, R.A., Elshire, R.J., Glaubitz, J.C., Guill, K.E., Kaeppler, S.M., et al., 2012. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808-811.

Kania, T., Russenberger, D., Peng, S., Apel, K., Melzer, S., 1997. FPF1 promotes flowering in Arabidopsis. Plant Cell 9, 1327-1338.

Korf, I., 2004. Gene finding in novel genomes. BMC Bioinform. 5, 59.

Kozlov, A.M., Darriba, D., Flouri, T., Morel, B., Stamatakis, A., 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453-4455.

Krawinkel, M.B., Ludwig, C., Swai, M.E., Yang, R.-y., Chun, K.P., Habicht, S.D., 2018. Bitter gourd reduces elevated fasting plasma glucose levels in an intervention study among prediabetics in Tanzania. J. Ethnopharmacol. 216, 1-7.

Le, S., Josse, J., Husson, F., 2008. FactoMineR: an R package for multivariate analysis. J. Stat. Softw. 25, 1-18.

Li, H., Durbin, R., 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595.

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.

Li, M.-X., Yeung, J.M.Y., Cherny, S.S., Sham, P.C., 2012. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum. Genet. 131, 747-756.

Li, W., Wang, H., Yu, D., 2016. Arabidopsis WRKY transcription factors WRKY12 and WRKY13 oppositely regulate flowering under short-day conditions. Mol. Plant 9, 1492-1503.

Lin, Y.-S., Huang, W.-Y., Ho, P.-Y., Hu, S.-Y., Lin, Y.-Y., Chen, C.-Y., Chang, M.-Y., Huang, S.-L., 2020. Effects of storage time and temperature on antioxidants in juice from Momordica charantia L. and Momordica charantia L. var. abbreviata Ser. Molecules 25, 3614.

Lin, Y., Ye, C., Li, X., Chen, Q., Wu, Y., Zhang, F., Pan, R., Zhang, S., Chen, S., Wang, X., et al., 2023. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Hortic. Res. 10, uhad127.

Ling, J., Jiang, W., Zhang, Y., Yu, H., Mao, Z., Gu, X., Huang, S., Xie, B., 2011. Genome-wide analysis of WRKY gene family in Cucumis sativus. BMC Genomics 12, 471.

Liu, D., Sun, W., Yuan, Y., Zhang, N., Hayward, A., Liu, Y., Wang, Y., 2014. Phylogenetic analyses provide the first insights into the evolution of OVATE family proteins in land plants. Ann. Bot. 113, 1219-1233.

Liu, X., Dong, S., Miao, H., Bo, K., Li, C., Yang, Y., Gu, X., Zhang, S., 2022. Genome-wide analysis of expansins and their role in fruit spine development in cucumber (Cucumis sativus L.). Hortic. Plant J. 8, 757-768.

Ma, L., Wang, Q., Mu, J., Fu, A., Wen, C., Zhao, X., Gao, L., Li, J., Shi, K., Wang, Y., et al., 2020. The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. Hortic. Res. 7, 199.

Ma, L., Wang, Q., Zheng, Y., Guo, J., Yuan, S., Fu, A., Bai, C., Zhao, X., Zheng, S., Wen, C., et al., 2022. Cucurbitaceae genome evolution, gene function, and molecular breeding. Hortic. Res. 9, uhab057.

Manni, M., Berkeley, M.R., Seppey, M., Simao, F.A., Zdobnov, E.M., 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647-4654.

Marcais, G., Kingsford, C., 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-770.

Matsumura, H., Hsiao, M.-C., Lin, Y.-P., Toyoda, A., Taniai, N., Tarora, K., Urasaki, N., Anand, S.S., Dhillon, N.P.S., Schafleitner, R., et al., 2020. Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication. Proc. Natl. Acad. Sci. U. S. A. 117, 14543-14551.

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al., 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.

Melzer, S., Lens, F., Gennen, J., Vanneste, S., Rohde, A., Beeckman, T., 2008. Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana. Nat. Genet. 40, 1489-1492.

Meyer, R.S., Purugganan, M.D., 2013. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840-852.

Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., Gurevich, A., 2018. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34, i142-i150.

Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., von Haeseler, A., Lanfear, R., 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530-1534.

Montero-Pau, J., Blanca, J., Bombarely, A., Ziarsolo, P., Esteras, C., Marti-Gomez, C., Ferriol, M., Gomez, P., Jamilena, M., Mueller, L., et al., 2018. De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus. Plant Biotechnol. J. 16, 1161-1171.

Murray, M.G., Thompson, W.F., 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321-4326.

Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J.R.A., Hellinga, A.J., Lugo, C.S.B., Elliott, T.A., Ware, D., Peterson, T., et al., 2019. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20, 275.

Pan, Y., Wang, Y., McGregor, C., Liu, S., Luan, F., Gao, M., Weng, Y., 2020. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. Theor. Appl. Genet. 133, 1-21.

Pichot, C., Djari, A., Tran, J., Verdenaud, M., Marande, W., Huneau, C., Gautier, V., Latrasse, D., Arribat, S., Sommard, V., et al., 2022. Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype. iScience 25, 103696.

Pootakham, W., Sonthirod, C., Naktang, C., Nawae, W., Yoocha, T., Kongkachana, W., Sangsrakru, D., Jomchai, N., U-thoomporn, S., Sheedy, J.R., et al., 2021. De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements. Mol. Ecol. Resour. 21, 212-225.

Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., et al., 2013. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat. Genet. 45, 1510-1515.

Qin, X., Zhang, Z., Lou, Q., Xia, L., Li, J., Li, M., Zhou, J., Zhao, X., Xu, Y., Li, Q., et al., 2021. Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber. Hortic. Res. 8, 40.

Quinlan, A.R., Hall, I.M., 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.

Rehman, S., Bahadur, S., Xia, W., 2024. Unlocking nature's secrets: the pivotal role of WRKY transcription factors in plant flowering and fruit development. Plant Sci. 346, 112150.

Renner, S.S., 2020. Bitter gourd from Africa expanded to Southeast Asia and was domesticated there: a new insight from parallel studies. Proc. Natl. Acad. Sci. U. S. A. 117, 24630-24631.

Renner, S.S., Wu, S., Perez-Escobar, O.A., Silber, M.V., Fei, Z., Chomicki, G., 2021. A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Proc. Natl. Acad. Sci. U. S. A. 118, e2101486118.

Robatzek, S., Somssich, I.E., 2002. Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev. 16, 1139-1149.

Saxena, S., Singh, A., Archak, S., Behera, T.K., John, J.K., Meshram, S.U., Gaikwad, A.B., 2015. Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability. Appl. Biochem. Biotechnol. 175, 93-118.

Schaefer, H., Renner, S.S., 2010. A three-genome phylogeny of Momordica (Cucurbitaceae) suggests seven returns from dioecy to monoecy and recent long-distance dispersal to Asia. Mol. Phylogenet. Evol. 54, 553-560.

Shi, X., Cao, S., Wang, X., Huang, S., Wang, Y., Liu, Z., Liu, W., Leng, X., Peng, Y., Wang, N., et al., 2023. The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Hortic. Res. 10, uhad061.

Slater, G.S.C., Birney, E., 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinform. 6, 31.

Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., Morgenstern, B., 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435-W439.

Sun, H., Wu, S., Zhang, G., Jiao, C., Guo, S., Ren, Y., Zhang, J., Zhang, H., Gong, G., Jia, Z., et al., 2017. Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes. Mol. Plant 10, 1293-1306.

Sur, S., Ray, R.B., 2020. Bitter melon (Momordica charantia), a nutraceutical approach for cancer prevention and therapy. Cancers 12, 2064.

Takagi, H., Lee, N., Hempton, A.K., Purushwani, S., Notaguchi, M., Yamauchi, K., Shirai, K., Kawakatsu, Y., Uehara, S., Albers, W.G., et al., 2025. Florigen-producing cells express FPF1-LIKE PROTEIN 1 to accelerate flowering and stem growth in Arabidopsis. Dev. Cell 60, 1822-1837.e8.

Tan, M.-J., Ye, J.-M., Turner, N., Hohnen-Behrens, C., Ke, C.-Q., Tang, C.-P., Chen, T., Weiss, H.-C., Gesing, E.-R., Rowland, A., et al., 2008. Antidiabetic activities of triterpenoids isolated from bitter melon associated with activation of the AMPK pathway. Chem. Biol. 15, 263-273.

Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y., Borodovsky, M., 2008. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 18, 1979-1990.

Urasaki, N., Takagi, H., Natsume, S., Uemura, A., Taniai, N., Miyagi, N., Fukushima, M., Suzuki, S., Tarora, K., Tamaki, M., et al., 2016. Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions. DNA Res. 24, 51-58.

Vurture, G.W., Sedlazeck, F.J., Nattestad, M., Underwood, C.J., Fang, H., Gurtowski, J., Schatz, M.C., 2017. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202-2204.

Wang, D., Zhang, Y., Zhang, Z., Zhu, J., Yu, J., 2010. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinform. 8, 77-80.

Wang, J., Sun, P., Li, Y., Liu, Y., Yang, N., Yu, J., Ma, X., Sun, S., Xia, R., Liu, X., et al., 2017. An overlooked paleotetraploidization in Cucurbitaceae. Mol. Biol. Evol. 35, 16-26.

Wang, M., Cao, Z., Jiang, B., Wang, K., Xie, D., Chen, L., Shi, S., Yang, S., Lu, H., Peng, Q., 2024. Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua. Hortic. Res. 11, uhae113.

Wang, S., Chang, Y., Guo, J., Chen, J.-G., 2007. Arabidopsis ovate family protein 1 is a transcriptional repressor that suppresses cell elongation. Plant J. 50, 858-872.

Wang, S., Chang, Y., Guo, J., Zeng, Q., Ellis, B.E., Chen, J.-G., 2011. Arabidopsis ovate family proteins, a novel transcriptional repressor family, control multiple aspects of plant growth and development. PLOS ONE 6, e23896.

Wang, Y., Tang, H., DeBarry, J.D., Tan, X., Li, J., Wang, X., Lee, T.-h., Jin, H., Marler, B., Guo, H., et al., 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49.

Wolff, J., Backofen, R., Gruning, B., 2022. Loop detection using Hi-C data with HiCExplorer. GigaScience 11, giac061.

Wu, S., Shamimuzzaman, M., Sun, H., Salse, J., Sui, X., Wilder, A., Wu, Z., Levi, A., Xu, Y., Ling, K.S., et al., 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.

Xia, M., Han, X., He, H., Yu, R., Zhen, G., Jia, X., Cheng, B., Deng, X.-W., 2018. Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo. GigaScience 7, giy067.

Xie, D., Xu, Y., Wang, J., Liu, W., Zhou, Q., Luo, S., Huang, W., He, X., Li, Q., Peng, Q., et al., 2019. The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype. Nat. Commun. 10, 5158.

Xie, Z., Zhang, Z.-L., Zou, X., Yang, G., Komatsu, S., Shen, Q.J., 2006. Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Plant J. 46, 231-242.

Xu, P., Wang, Y., Sun, F., Wu, R., Du, H., Wang, Y., Jiang, L., Wu, X., Wu, X., Yang, L., et al., 2021. Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd. Plant J. 107, 956-968.

Xu, S., Hu, E., Cai, Y., Xie, Z., Luo, X., Zhan, L., Tang, W., Wang, Q., Liu, B., Wang, R., et al., 2024a. Using clusterProfiler to characterize multiomics data. Nat. Protoc. 19, 3292-3320.

Xu, X., Du, Y., Li, S., Tan, M., Sohail, H., Liu, X., Qi, X., Yang, X., Chen, X., 2024b. A genome-wide association study reveals molecular mechanism underlying powdery mildew resistance in cucumber. Genome Biol. 25, 252.

Yang, J., Lee, S.H., Goddard, M.E., Visscher, P.M., 2011. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76-82.

Yang, Z., 2007. PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591.

Yin, L., Zhang, H., Tang, Z., Xu, J., Yin, D., Zhang, Z., Yuan, X., Zhu, M., Zhao, S., Li, X., et al., 2021. rMVP: a memory-efficient, visualization-enhanced, and parallel-accelerated tool for genome-wide association study. Genomics Proteomics Bioinform. 19, 619-628.

Zhang, B., Li, Q., Keyhaninejad, N., Taitano, N., Sapkota, M., Snouffer, A., van der Knaap, E., 2023. A combinatorial TRM-OFP module bilaterally fine-tunes tomato fruit shape. New Phytol. 238, 2393-2409.

Zhang, C., Dong, S.S., Xu, J.Y., He, W.M., Yang, T.L., 2019. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786-1788.

Zhang, T., Ren, X., Zhang, Z., Ming, Y., Yang, Z., Hu, J., Li, S., Wang, Y., Sun, S., Sun, K., et al., 2020. Long-read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome. Mol. Ecol. Resour. 20, 511-519.

Zhang, Y., Zhao, M., Tan, J., Huang, M., Chu, X., Li, Y., Han, X., Fang, T., Tian, Y., Jarret, R., et al., 2024. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat. Genet. 56, 1750-1761.

Zhang, Z., Xiao, J., Wu, J., Zhang, H., Liu, G., Wang, X., Dai, L., 2012. ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem. Biophys. Res. Commun. 419, 779-781.

Zhao, G., Lian, Q., Zhang, Z., Fu, Q., He, Y., Ma, S., Ruggieri, V., Monforte, A.J., Wang, P., Julca, I., et al., 2019. A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nat. Genet. 51, 1607-1615.

Relative Articles

Supplements(0)

Cited By

Proportional views