Alexa A, Rahnenfuhrer J, Lengauer T. 2006. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics, 22, 1600–1607.

Arunraj R, Skori L, Kumar A, Hickerson N M N, Shoma N, Vairamani M, Samuel M A. 2020. Spatial regulation of alpha-galactosidase activity and its influence on raffinose family oligosaccharides during seed maturation and germination in Cicer arietinum. Plant Signaling & Behavior, 15, 1709707.

Blum M, Chang H Y, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar G A, Williams L, Bork P, Bridge A, Gough J, Haft D H, Letunic I, Marchler-Bauer A, Mi H Y, et al. 2021. The InterPro protein families and domains database: 20 years on. Nucleic Acids Research, 49, D344–D354.

Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.

Bood K G, Zabetakis I. 2002. The biosynthesis of strawberry flavor (II): Biosynthetic and molecular biology studies. Journal of Food Science, 67, 2–8.

Buchfink B, Xie C, Huson D H. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12, 59–60.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden T L. 2009. BLAST+: Architecture and applications. BMC Bioinformatics, 10, 9.

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. Molecular Biology and Evolution, 38, 5825–5829.

Cao Y, Han Y, Meng D, Li D, Jin Q, Lin Y, Cai Y. 2016. Structural, evolutionary, and functional analysis of the class III peroxidase gene family in Chinese pear (Pyrus bretschneideri). Frontiers in Plant Science, 7, 1874.

Chen X N, Zhang M Y, Sun M Y, Liu Y Y, Li S N, Song B B, Li M Y, Zhang S L, Wang R Z, Li J M, Zhao K J, Wu J. 2022. Genome-wide genetic diversity and IBD analysis reveals historic dissemination routes of pear in China. Tree Genet Genomes, 18,1–12.

Cramer C S, Wehner T C. 2000. Path analysis of the correlation between fruit number and plant traits of cucumber populations. Hortscience, 35, 708–711.

Deng Y W, Ning Y S, Yang D L, Zhai K R, Wang G L, He Z H. 2020. Molecular basis of disease resistance and perspectives on breeding strategies for resistance improvement in crops. Molecular Plant, 13, 1402–1419.

Friedrich L, Moyer M, Ward E, Ryals J. 1991. Pathogenesis-related protein 4 is structurally homologous to the carboxy-terminal domains of hevein, win-1 and win-2. Molecular and General Genetics MGG, 230, 113–119.

Gao L, Gonda I, Sun H H, Ma Q Y, Bao K, Tieman D M, Burzynski-Chang E A, Fish T L, Stromberg K A, Sacks G L, Thannhauser T W, Foolad M R, Diez M J, Blanca J, Canizares J, Xu Y M, van der Knaap E, Huang S W, Klee H J, Giovannoni J J, et al. 2019. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 51, 1044–1051.

Gao Y H, Yang Q S, Yan X H, Wu X Y, Yang F, Li J Z, Wei J, Ni J B, Ahmad M, Bai S L, Teng Y W. 2021. High-quality genome assembly of ‘Cuiguan’ pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy. Horticulture Research, 8, 197.

Ginestet C. 2011. ggplot2: Elegant graphics for data analysis. Journal of the Royal Statistical Society Series A: Statistics in Society, 174, 245–246.

Golicz A A, Batley J, Edwards D. 2016. Towards plant pangenomics. Plant Biotechnology Journal, 14, 1099–1105.

Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q D, Chen Z H, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren B W, Nusbaum C, Lindblad-Toh K, Friedman N, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644–652.

Hirsch C N, Foerster J M, Johnson J M, Sekhon R S, Muttoni G, Vaillancourt B, Penagaricano F, Lindquist E, Pedraza M A, Barry K, de Leon N, Kaeppler S M, Buell C R. 2014. Insights into the maize pan-genome and pan-transcriptome. Plant Cell, 26, 121–135.

Islam F M A, Rengifo J, Redden R J, Basford K E, Beebe S E. 2003. Association between seed coat polyphenolics (tannins) and disease resistance in common bean. Plant Foods for Human Nutrition, 58, 285–297.

Jiang Z, Tang F, Huang H, Hu H, Chen Q. 2009. Assessment of genetic diversity of Chinese sand pear landraces (Pyrus pyrifolia Nakai) using simple sequence repeat markers. HortScience, 44, 619–626.

Jin J P, Tian F, Yang D C, Meng Y Q, Kong L, Luo J C, Gao G. 2017. PlantTFDB 4.0: Toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, 45, D1040-D1045.

Jin M L, Liu H J, He C, Fu J J, Xiao Y J, Wang Y B, Xie W B, Wang G Y, Yan J B. 2016. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Scientific Reports, 6, 1–12.

Jones P, Binns D, Chang H Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn A F, Sangrador-Vegas A, Scheremetjew M, Yong S Y, Lopez R, Hunter S. 2014. InterProScan 5: Genome-scale protein function classification. Bioinformatics, 30, 1236–1240.

Jungo F, Bougueleret L, Xenarios I, Poux S. 2012. The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. Toxicon, 60, 551–557.

Khan A, Korban S S. 2022. Breeding and genetics of disease resistance in temperate fruit trees: Challenges and new opportunities. Theoretical and Applied Genetics, 135, 3961–3985.

Kong W L, Jiang M W, Wang Y B, Chen S, Zhang S C, Lei W L, Chai K, Wang P J, Liu R Y, Zhang X T. 2022. Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis. Horticulture Research, 9, uhac100.

Kuznetsova I, Lugmayr A, Siira S J, Rackham O, Filipovska A. 2019. CirGO: An alternative circular way of visualising gene ontology terms. BMC Bioinformatics, 20, 1–7.

Langfelder P, Horvath S. 2008. WGCNA: An R package for weighted correlation network analysis. Bmc Bioinformatics, 9, 559.

Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359.

Lee J H, Venkatesh J, Jo J, Jang S, Kim G W, Kim J M, Han K, Ro N, Lee H Y, Kwon J K, Kim Y M, Lee T H, Choi D, Van Deynze A, Hill T, Kfir N, Freiman A, Olivas N H D, Elkind Y, Paran I, et al. 2022. High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers. Horticulture Research, 9, uhac210.

Leek J T, Johnson W E, Parker H S, Jaffe A E, Storey J D. 2012. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics, 28, 882–883.

Li J M, Zhang M Y, Li X L, Khan A, Kumar S, Allan A C, Kui L W, Espley R V, Wang C H, Wang R Z, Xue C, Yao G F, Qin M F, Sun M Y, Tegtmeier R, Liu H N, Wei W L, Ming M L, Zhang S L, Zhao K J, Song B B, Ni J P, An J P, Korban S S, Wu J. 2022. Pear genetics: Recent advances, new prospects, and a roadmap for the future. Horticulture Research, 9, uhab040.

Li J M, Zheng D M, Li L T, Qiao X, Wei S W, Bai B, Zhang S L, Wu J. 2015. Genome-wide function, evolutionary characterization and expression analysis of sugar transporter family genes in pear (Pyrus bretschneideri Rehd). Plant and Cell Physiology, 56, 1721–1737.

Li M, Dunwell J M, Zhang H W, Wei S W, Li Y J, Wu J Y, Zhang S L. 2018. Network analysis reveals the co-expression of sugar and aroma genes in the Chinese white pear (Pyrus bretschneideri). Gene, 677, 370–377.

Li W, Godzik A. 2006. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658–1659.

Li X L, Liu L, Ming M L, Hu H J, Zhang M Y, Fan J, Song B B, Zhang S L, Wu J. 2019. Comparative transcriptomic analysis provides insight into the domestication and improvement of pear (P. pyrifolia) fruit. Plant Physiology, 180, 435–452.

Li X L, Xue C, Li J M, Qiao X, Li L T, Yu L A, Huang Y H, Wu J. 2016. Genome-wide identification, evolution and functional divergence of myb transcription factors in Chinese white pear (Pyrus bretschneideri). Plant and Cell Physiology, 57, 824–847.

Little D, Gouhier-Darimont C, Bruessow F, Reymond P. 2007. Oviposition by pierid butterflies triggers defense responses in Arabidopsis. Plant Physiology, 143, 784–800.

Liu D, Yang L, Zhang J Z, Zhu G T, Lu H J, Lu Y Q, Wang Y L, Cao X, Sun T S, Huang S W, Wu Y Y. 2020. Domestication and breeding changed tomato fruit transcriptome. Journal of Integrative Agriculture, 19, 120–132.

Liu H M, Liu Z J, Wu Y, Zheng L M, Zhang G F. 2021. Regulatory mechanisms of anthocyanin biosynthesis in apple and pear. International Journal of Molecular Sciences, 22, 8441.

Liu S R, An Y L, Tong W, Qin X J, Samarina L, Guo R, Xia X B, Wei C L. 2019. Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research. BMC Genomics, 20, 1–16.

Love M I, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550.

Ma Y L, Liu M, Stiller J, Liu C J. 2019. A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. BMC Genomics, 20, 1–11.

Moing A, Poessel J L, Svanella-Dumas L, Loonis M, Kervella J. 2003. Biochemical basis of low fruit quality of Prunus davidiana, a pest and disease resistance donor for peach breeding. Journal of the American Society for Horticultural Science, 128, 55–62.

Nguyen L T, Schmidt H A, von Haeseler A, Minh B Q. 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268–274.

Nicolai M, Roncato M A, Canoy A S, Rouquie D, Sarda X, Freyssinet G, Robaglia C. 2006. Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiology, 141, 663–673.

O’Leary N A, Wright M W, Brister J R, Ciufo S, McVeigh D H R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y M, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell C M, Goldfarb T, et al. 2016. Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44, D733–D745.

Oshlack A, Wakefield M J. 2009. Transcript length bias in RNA-seq data confounds systems biology. Biology Direct, 4, 14.

Ou C Q, Zhang X L, Wang F, Zhang L Y, Zhang Y J, Fang M, Wang J H, Wang J X, Jiang S L, Zhang Z H. 2020. A 14 nucleotide deletion mutation in the coding region of the PpBBX24 gene is associated with the red skin of “Zaosu Red” pear (Pyrus pyrifolia White Pear Group): A deletion in the PpBBX24 gene is associated with the red skin of pear. Horticulture Research, 7, 39.

Ou LJ, Li D, Lv J H, Chen W C, Zhang Z Q, Li X F, Yang B Z, Zhou S D, Yang S, Li W G, Gao H Z, Zeng Q, Yu H Y, Ouyang B, Li F, Liu F, Zheng J Y, Liu Y H, Wang J, Wang B B, et al. 2018. Pan-genome of cultivated pepper (Capsicum) and its use in gene presence-absence variation analyses. New Phytologist, 220, 360–363.

Pillich R T, Chen J, Rynkov V, Welker D, Pratt D. 2017. NDEx: A community resource for sharing and publishing of biological networks. Protein Bioinformatics: From Protein Modifications and Networks to Proteomics, 1558, 271–301.

Prunier J, Giguere I, Ryan N, Guy R, Soolanayakanahally R, Isabel N, MacKay J, Porth I. 2019. Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations. Molecular Ecology, 28, 1476–1490.

do Rego E R, do Rego M M, Cruz C D, Finger F L, Casali V W D. 2011. Phenotypic diversity, correlation and importance of variables for fruit quality and yield traits in Brazilian peppers (Capsicum baccatum). Genetic Resources Crop Evolution, 58, 909–918.

Ruan J, Dean A K, Zhang W. 2010. A general co-expression network-based approach to gene expression analysis: Comparison and applications. BMC Systems Biology, 4, 8.

Saito T. 2016. Advances in Japanese pear breeding in Japan. Breeding Science, 66, 46–59.

Schwab W, Davidovich-Rikanati R, Lewinsohn E. 2008. Biosynthesis of plant-derived flavor compounds. The Plant Journal, 54, 712–732.

Shan Y F, Li M Y, Wang R Z, Li X G, Jing L, Li J M, Zhao K J, Jun W. 2023. Evaluation of the early defoliation trait and identification of resistance genes through a comprehensive transcriptome analysis in pears. Journal of Integrative Agriculture, 22, 120–138.

Shannon P, Markiel A, Ozier O, Baliga N S, Wang J T, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498–2504.

Shirasawa K, Itai A, Isobe S. 2021. Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’. DNA Research, 28, dsab001.

Song Y, Fan L, Chen H, Zhang M Y, Ma Q Q, Zhang S L, Wu J. 2014. Identifying genetic diversity and a preliminary core collection of Pyrus pyrifolia cultivars by a genome-wide set of SSR markers. Scientia Horticulture, 167, 5–16.

Stoeckli S, Mody K, Dorn S, Kellerhals M. 2011. Association between herbivore resistance and fruit quality in apple. Hortscience, 46, 12–15.

Su J S, Zhang F, Chong X R, Song A P, Guan Z Y, Fang W M, Chen F D. 2019. Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums. Horticulture Research, 6, 21.

Sun C, Fu D, Lu H P, Zhang J H, Zheng X D, Yu T. 2018. Autoclaved yeast enhances the resistance against Penicillium expansum in postharvest pear fruit and its possible mechanisms of action. Biological Control, 119, 51–58.

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

Sun Y Q, Shang L G, Zhu Q H, Fan L J, Guo L B. 2022. Twenty years of plant genome sequencing: Achievements and challenges. Trends in Plant Science, 27, 391–401.

Supek F, Bosnjak M, Skunca N, Smuc T. 2011. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE, 6, e21800.

Tettelin H, Masignani V, Cieslewicz M J, Donati C, Medini D, Ward N L, Angiuoli S V, Crabtree J, Jones A L, Durkin A S, DeBoy R T, Davidsen T M, Mora M, Scarselli M, Ros I M Y, Peterson J D, Hauser C R, Sundaram J P, Nelson W C, Madupu R, et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”. Proceedings of the National Academy of Sciences of the United States of America, 102, 13950–13955.

Tettelin H, Riley D, Cattuto C, Medini D. 2008. Comparative genomics: The bacterial pan-genome. Current Opinion in Microbiology, 11, 472–477.

Wang R Z, Xue Y S, Fan J, Yao J L, Qin M F, Lin T, Lian Q, Zhang M Y, Li X L, Li J M, Sun M Y, Song B B, Zhang J Y, Zhao K J, Chen X, Hu H J, Fei Z J, Xue C, Wu J. 2021. A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit. Genome Biology, 22, 1–23.

Wang X Q, Wang H H, Shi C H, Zhang X Y, Duan K, Luo J. 2015. Morphological, cytological and fertility consequences of a spontaneous tetraploid of the diploid pear (Pyrus pyrifolia Nakai) cultivar ‘Cuiguan’. Scientia Horticulturae, 189, 59–65.

Wei H B, Bausewein A, Greiner S, Dauchot N, Harms K, Rausch T. 2017. CiMYB17, a stress-induced chicory R2R3-MYB transcription factor, activates promoters of genes involved in fructan synthesis and degradation. New Phytologist, 215, 281–298.

Wu J, Wang Y, Xu J, Korban S S, Fei Z, Tao S, Ming R, Tai S, Khan A M, Postman J D, Gu C, Yin H, Zheng D, Qi K, Li Y, Wang R, Deng C H, Kumar S, Chagné D, et al. 2018. Diversification and independent domestication of Asian and European pears. Genome Biology, 19, 1–16.

Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan M A, Tao S, Korban S S, Wang H, Chen N J, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, et al. 2013. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Research, 23, 396–408.

Wu Q, Tong W, Zhao H J, Ge R H, Li R P, Huang J, Li F D, Wang Y L, Mallano A I, Deng W W, Wang W J, Wan X C, Zhang Z Z, Xia E H. 2022. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. The Plant Journal, 111, 406–421.

Wu T D, Watanabe C K. 2005. GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859–1875.

Xue C, Yao J L, Qin M F, Zhang M Y, Allan A C, Wang D F, Wu J. 2019a. PbrmiR397a regulates lignification during stone cell development in pear fruit. Plant Biotechnology Journal, 17, 103–117.

Xue C, Yao J L, Xue Y S, Su G Q, Wang L, Lin L K, Allan A C, Zhang S L, Wu J. 2019b. PbrMYB169 positively regulates lignification of stone cells in pear fruit. Journal of Experimental Botany, 70, 1801–1814.

Yan Y, Zheng X F, Apaliya M T, Yang H J, Zhang H. 2018. Transcriptome characterization and expression profile of defense-related genes in pear induced by Meyerozyma guilliermondii. Postharvest Biology and Technology, 141, 63–70.

Yu G C, Wang L G, Han Y Y, He Q Y. 2012. clusterProfiler: An R package for comparing biological themes among gene clusters. Omics: A Journal of Integrative Biology, 16, 284–287.

Zhang M Y, Xue C, Hu H J, Li J M, Xue Y S, Wang R Z, Fan J, Zou C, Tao S T, Qin M F, Bai B, Li X L, Gu C, Wu S, Chen X, Yang G Y, Liu Y Y, Sun M Y, Fei Z J, Zhang S L, et al. 2021. Genome-wide association studies provide insights into the genetic determination of fruit traits of pear. Nature Communications, 12, 1144.

Zhang Y, Butelli E, Alseekh S, Tohge T, Rallapalli G, Luo J, Kawar P G, Hill L, Santino A, Fernie A R, Martin C. 2015. Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. Nature Communications, 6, 8635.

Zhao B Y, Qi K J, Yi X R, Chen G D, Liu X, Qi X X, Zhang S L. 2019. Identification of hexokinase family members in pear (Pyrus×bretschneideri) and functional exploration of PbHXK1 in modulating sugar content and plant growth. Gene, 711, 143932.

Zhao Q, Feng Q, Lu H Y, Li Y, Wang A, Tian Q L, Zhan Q L, Lu Y Q, Huang T, Wang Y C, Fan D L, Zhao Y, Wang Z Q, Zhou C C, Chen J Y, Zhu C R, Li W J, Weng Q J, Xu Q, Wang Z X, et al. 2018. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nature Genetics, 50, 278–284.