Alioto T, Alexiou K G, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Martí A F I, Frias L, Galán B, García J L, Howad W, Gómez-Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Cabetas M J R, et al. 2020. Transposons played a major role in the diversification between the closely related almond and peach genomes: Results from the almond genome sequence. Plant Journal, 101, 455–472.

Blazek J, Zeleny L, Suran P. 2022. Sweet cherry research world overview 2015–2017. Horticultural Science, 49, 121–146.

Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C. 2012. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell, 24, 1242–1255.

Calle A, Wünsch A. 2020. Multiple-population QTL mapping of maturity and fruit-quality traits reveals LG4 region as a breeding target in sweet cherry (Prunus avium L.). Horticulture Research, 7, 127.

Cao K, Yang X, Li Y, Zhu G, Fang W, Chen C, Wang X, Wu J, Wang L. 2021. New high-quality peach (Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits. Plant Journal, 108, 281–295.

Castillejo C, Waurich V, Wagner H, Ramos R, Oiza N, Muñoz P, Triviño J C, Caruana J, Liu Z, Cobo N, Hardigan M A, Knapp S J, Vallarino J G, Osorio S, Martín-Pizarro C, Posé D, Toivainen T, Hytönen T, Oh Y, Barbey C R, et al. 2020. Allelic variation of MYB10 is the major force controlling natural variation in skin and flesh color in strawberry (Fragaria spp.) fruit. Plant Cell, 32, 3723–3749.

Chagné D, Kui L W, Espley R V, Volz R K, How N M, Rouse S, Brendolise C, Carlisle C M, Kumar S, De Silva N, Micheletti D, McGhie T, Crowhurst R N, Storey R D, Velasco R, Hellens R P, Gardiner S E, Allan A C. 2013. An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiology, 161, 225–239.

Cheng H, Concepcion G T, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods, 18, 170–175.

Danecek P, Bonfield J K, Liddle J, Marshall J, Ohan V, Pollard M O, Whitwham A, Keane T, McCarthy S A, Davies R M, Li H. 2021. Twelve years of SAMtools and BCFtools. Gigascience, 10, giab008.

Dong Y X, Qi X L, Liu C L, Song L L, Ming L. 2022. A sweet cherry AGAMOUS-LIKE transcription factor PavAGL15 affects fruit size by directly repressing the PavCYP78A9 expression. Scientia Horticulturae, 297, 110947.

Donkpegan A S, Bernard A, Barreneche T, Quero-García J, Bonnet H, Fouché M, Le Dantec L, Wenden B, Dirlewanger E. 2023. Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits. Horticulture Research, 10, uhad191.

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, Aiden E L. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356, 92–95.

Durand N C, Shamim M S, Machol I, Rao S S, Huntley M H, Lander E S, Aiden E L. 2016. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems, 3, 95–98.

Edger P P, Poorten T J, VanBuren R, Hardigan M A, Colle M, McKain M R, Smith R D, Teresi S J, Nelson D L, Wai C M, Alger E I, Bird K A, Yocca A E, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, et al. 2019. Origin and evolution of the octoploid strawberry genome. Nature Genetics, 51, 541–547.

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

Espley R V, Brendolise C, Chagné D, Kutty-Amma S, Green S, Volz R, Putterill J, Schouten H J, Gardiner S E, Hellens R P, Allan A C. 2009. Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. Plant Cell, 21, 168–183.

Fiol A, García-Gómez B E, Jurado-Ruiz F, Alexiou K, Howad W, Aranzana M J. 2021. Characterization of Japanese plum (Prunus salicina) PsMYB10 alleles reveals structural variation and polymorphisms correlating with fruit skin color. Frontiers in Plant Science, 12, 655267.

Foster T M, Celton J M, Chagné D, Tustin D S, Gardiner S E. 2015. Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple. Horticulture Research, 2, 15001.

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

Hoff K J, Stanke M. 2019. Predicting genes in single genomes with AUGUSTUS. Current Protocols in Bioinformatics, 65, e57.

Holusova K, Cmejlova J, Suran P, Cmejla R, Sedlak J, Zeleny L, Bartos J. 2023. High-resolution genome-wide association study of a large Czech collection of sweet cherry (Prunus avium L.) on fruit maturity and quality traits. Horticulture Research, 10, uhac233.

Huang D, Wang X, Tang Z, Yuan Y, Xu Y, He J, Jiang X, Peng S A, Li L, Butelli E, Deng X, Xu Q. 2018. Subfunctionalization of the Ruby2-Ruby1 gene cluster during the domestication of citrus. Nature Plants, 4, 930–941.

Hubley R, Finn R D, Clements J, Eddy S R, Jones T A, Bao W, Smit A F, Wheeler T J. 2016. The Dfam database of repetitive DNA families. Nucleic Acids Research, 44, D81–D89.

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund S K, Cook H, Mende D R, Letunic I, Rattei T, Jensen L J, von Mering C, Bork P. 2019. eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47, D309–D314.

Jin W, Wang H, Li M, Wang J, Yang Y, Zhang X, Yan G, Zhang H, Liu J, Zhang K. 2016. The R2R3 MYB transcription factor PavMYB10.1 involves in anthocyanin biosynthesis and determines fruit skin colour in sweet cherry (Prunus avium L.). Plant Biotechnology Journal, 14, 2120–2133.

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

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A. 2009. Circos: An information aesthetic for comparative genomics. Genome Research, 19, 1639–1645.

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

Kui L W, Bolitho K, Grafton K, Kortstee A, Karunairetnam S, McGhie T K, Espley R V, Hellens RP, Allan A C. 2010. An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biology, 10, 50.

Lin Y, Ye C, Li X, Chen Q, Wu Y, Zhang F, Pan R, Zhang S, Chen S, Wang X, Cao S, Wang Y, Yue Y, Liu Y, Yue J. 2023. quarTeT: A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Horticulture Research, 10, uhad127.

Liu C, Qi X, Song L, Chen L, Dong Y, Pan F, Zheng W, Li Y, Zhao B, Guo W, Li M, Wang Z. 2023. Large-fragment deletion encompasses the R2R3 MYB transcription factor, PavMYB10.1, causes yellow fruits in sweet cherry (Prunus avium L.). Scientia Horticulturae, 309, 111648.

Lomsadze A, Ter-Hovhannisyan V, Chernoff Y O, Borodovsky M. 2005. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research, 33, 6494–6506.

Majoros W H, Pertea M, Salzberg S L. 2004. TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders. BMC Bioinformatics, 20, 2878–2879.

Ou S, Chen J, Jiang N. 2018. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Research, 46, e126.

Rautiainen M, Nurk S, Walenz B P, Logsdon G A, Porubsky D, Rhie A, Eichler E E, Phillippy A M, Koren S. 2023. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nature Biotechnology, 41, 1474–1482.

Rhie A, Walenz B P, Koren S, Phillippy A M. 2020. Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology, 21, 245.

Seppey M, Manni M, Zdobnov E M. 2019. BUSCO: Assessing genome assembly and annotation completeness. Methods in Molecular Biolgy, 1962, 227–245.

Shen T J, Wen X P, Wen Z, Qiu Z L, Hou Q D, Li Z C, Mei L N, Yu H H, Qiao G. 2021. Genome-wide identification and expression analysis of bHLH transcription factor family in response to cold stress in sweet cherry (Prunus avium L.). Scientia Horticulturae, 279, 109905.

Shirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H, Isobe S. 2017. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Research, 24, 499–508.

Sooriyapathirana S S, Khan A, Sebolt A M, Wang D, Bushakra J M, Kui L W, Allan A C, Gardiner S E, Chagné D, Iezzoni A F. 2010. QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.). Tree Genetics & Genomes, 6, 821–832.

Sun C, Wang C, Zhang W, Liu S, Wang W, Yu X, Song T, Yu M, Yu W, Qu S. 2021. The R2R3-type MYB transcription factor MdMYB90-like is responsible for the enhanced skin color of an apple bud sport mutant. Horticulture Research, 8, 156.

Sun X, Jiao C, Schwaninger H, Chao C T, Ma Y, Duan N, Khan A, Ban S, Xu K, Cheng L, Zhong G Y, Fei Z. 2020. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nature Genetics, 52, 1423–1432.

Tang H, Bowers J E, Wang X, Ming R, Alam M, Paterson A H. 2008. Synteny and collinearity in plant genomes. Science, 320, 486–488.

Testa A C, Hane J K, Ellwood S R, Oliver R P. 2015. CodingQuarry: Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts. BMC Genomics, 16, 170.

Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori M T, Schmutz J. 2017. The Peach v2.0 release: High-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics, 18, 225.

Walker A R, Lee E, Bogs J, McDavid D A, Thomas M R, Robinson S P. 2007. White grapes arose through the mutation of two similar and adjacent regulatory genes. Plant Journal, 49, 772–785.

Wan T, Feng Y, Liang C L, Pan L Y, He L, Cai Y L. 2021. Metabolomics and transcriptomics analyses of two contrasting cherry rootstocks in response to drought stress. Biology-Basel, 10, 201.

Wang J, Liu W, Zhu D, Hong P, Zhang S, Xiao S, Tan Y, Chen X, Xu L, Zong X, Zhang L, Wei H, Yuan X, Liu Q. 2020. Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. Horticulture Research, 7, 122.

Wang J Y, Sun W X, Wang L, Liu X J, Xu Y, Sabir I A, Jiu S T, Wang S P, Zhang C X. 2022. FRUITFULL is involved in double fruit formation at high temperature in sweet cherry. Environmental and Experimental Botany, 201, 104986.

Wang L, Feng Y, Wang Y, Zhang J, Chen Q, Liu Z, Liu C, He W, Wang H, Yang S, Zhang Y, Luo Y, Tang H, Wang X. 2022. Accurate chromosome identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its relatives by Oligo-FISH. International Journal of Molecular Sciences, 23, 13213.

Wang Z, Meng D, Wang A, Li T, Jiang S, Cong P, Li T. 2013. The methylation of the PcMYB10 promoter is associated with green-skinned sport in Max Red Bartlett pear. Plant Physiology, 162, 885–896.

Wei H, Chen X, Zong X, Shu H, Gao D, Liu Q. 2015. Comparative transcriptome analysis of genes involved in anthocyanin biosynthesis in the red and yellow fruits of sweet cherry (Prunus avium L.). PLoS ONE, 10, e0121164.

Xu M, Guo L, Gu S, Wang O, Zhang R, Peters B A, Fan G, Liu X, Xu X, Deng L, Zhang Y. 2020. TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads. Gigascience, 9, giaa094.

Yue J, Chen Q, Wang Y, Zhang L, Ye C, Wang X, Cao S, Lin Y, Huang W, Xian H, Qin H, Wang Y, Zhang S, Wu Y, Wang S, Yue Y, Liu Y. 2023. Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis. Horticulture Research, 10, uhac264.

Zhang L, Hu J, Han X, Li J, Gao Y, Richards C M, Zhang C, Tian Y, Liu G, Gul H, Wang D, Tian Y, Yang C, Meng M, Yuan G, Kang G, Wu Y, Wang K, Zhang H, Wang D, et al. 2019. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature Communications, 10, 1494.

Zhou Q, Tang D, Huang W, Yang Z, Zhang Y, Hamilton J P, Visser R G F, Bachem C W B, Robin Buell C, Zhang Z, Zhang C, Huang S. 2020. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nature Genetics, 52, 1018–1023.

Zhou Y H, Xiong J S, Shu Z Q, Dong C, Gu T T, Sun P C, He S, Jiang M, Xia Z Q, Xue J Y, Khan W U, Chen F, Cheng Z M. 2023. The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry. Horticulture Research, 10, uhad027.