1 I. et al. Phylogenetic relationships and differentiation among and within populations of Chaenomeles Lindl. (Rosaceae) estimated with RAPDs and isozymes. TAG Theoretical&Applied Genetics (2000).
2 Song-jie, Y. Research Advances on Plant Germplasm Resources of Chaenomeles [J]. Hubei Agricultural Sciences 20 (2011).
3 Strek, M., Gorlach, S., Podsedek, A., Sosnowska, D. & Hrabec, E. Procyanidin Oligomers from Japanese Quince ( Chaenomeles japonica ) Fruit Inhibit Activity of MMP-2 and MMP-9 Metalloproteinases. Journal of Agricultural and Food Chemistry 55, 6447-6452 (2007).
4 Chen, R.-l., Wu, T.-j. & Dai, Y.-j. Studies on the Chemical Constiuents of Four Species of Chaenomeles. West China Journal of Pharmaceutical Sciences 15, 39-39 (2000).
5 Koehne, E. Gattungen der Pomaceen. (1890).
6 Morley, B. D. Augustine Henry: his botanical activities in China, 1882-1890. Glasra 3, 21-81 (1979).
7 Galan, R. & Palmer, J. The occurrence of the rare Ciboria aestivalis in Europe. CZECH MYCOLOGY 52, 277-288 (2000).
8 Potter, D. et al. Phylogeny and classification of Rosaceae. Plant systematics and evolution 266, 5-43 (2007).
9 Phipps, J. Mespilus canescens, a new Rosaceous endemic from Arkansas. Systematic botany, 26-32 (1990).
10 Phipps, J. B., Robertson, K. R., Rohrer, J. R. & Smith, P. G. Origins and Evolution of Subfam. Maloideae (Rosaceae). Systematic Botany 16, 303 (1991).
11 Rumpunen, K., Bartish, I., Garkavagustavsson, L. & Nybom, H. Molecular and morphological diversity in the plant genus Chaenomeles. (2003).
12 da Silva, J. A. T. et al. Santalum molecular biology: molecular markers for genetic diversity, phylogenetics and taxonomy, and genetic transformation. Agroforestry Systems 92, 1301-1315 (2018).
13 Chrungoo, N. et al. Establishing taxonomic identity and selecting genetically diverse populations for conservation of threatened plants using molecular markers. Current Science 114, 539 (2018).
14 Sharma, V. & Salwal, R. in Molecular Markers in Mycology 37-52 (Springer, 2017).
15 Bartish, I. V., Rumpunen, K. & Nybom, H. Combined analyses of RAPDs, cpDNA and morphology demonstrate spontaneous hybridization in the plant genus Chaenomeles. Heredity 85, 383-392 (2010).
16 He, J. et al. Genetic variability of cultivated Chaenomeles speciosa (Sweet) Nakai based on AFLP analysis. Biochemical Systematics & Ecology 57, 445-450 (2014).
17 Yan-Yan, Z. et al. Analysis of Genetic Diversity in Chaenomeles Using Apple EST-SSRs. Biotechnology Bulletin (2016).
18 Julio, E. et al. RNA-Seq analysis of Orobanche resistance in Nicotiana tabacum: development of molecular markers for breeding recessive tolerance from ‘Wika’tobacco variety. Euphytica 216, 6 (2020).
19 Thakur, O. & Randhawa, G. S. Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots. BMC genomics 19, 951 (2018).
20 Wu, N. et al. RNA-seq facilitates development of chromosome-specific markers and transfer of rye chromatin to wheat. Molecular breeding 38, 6 (2018).
21 Li, H., Ruan, C.-J., Wang, L., Ding, J. & Tian, X.-J. Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm. Journal of the American Society for Horticultural Science 142, 200-208 (2017).
22 Chen, H. (Master degree dissertation, Shandong Agricultural University, Tai’an.(in …, 2008).
23 Arnold, J. & Zhuge, R. Flora of China. (2007).
24 Carbone, I., Ramirez-Prado, J. H., Jakobek, J. L. & Horn, B. W. Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster. BMC Evolutionary Biology 7, 1-12 (2007).
25 Hurst, L. D. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends in genetics: TIG 18, 486-486 (2002).
26 Carbone, I., Jakobek, J. L., RAMIREZ‐PRADO, J. H. & Horn, B. W. Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus. Molecular Ecology 16 (2007).
27 Fukazawa, J. et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. The Plant cell 26, 2920-2938 (2014).
28 Fujikura, U., Horiguchi, G., Ponce, M. R., Micol, J. L. & Tsukaya, H. Coordination of cell proliferation and cell expansion mediated by ribosome-related processes in the leaves of Arabidopsis thaliana. Plant Journal 59, 499-508 (2010).
29 Bertini, L. et al. Modular structure of HEL protein from Arabidopsis reveals new potential functions for PR-4 proteins. Biological Chemistry 393, 1533-1546 (2012).
30 Geraldo, N., Bäurle, I., Kidou, S.-i., Hu, X. & Dean, C. FRIGIDA delays flowering in Arabidopsis via a cotranscriptional mechanism involving direct interaction with the nuclear cap-binding complex. Plant Physiology 150, 1611-1618 (2009).
31 Faigon-Soverna, A. et al. A Constitutive Shade-Avoidance Mutant Implicates TIR-NBS-LRR Proteins in Arabidopsis Photomorphogenic Development. The Plant cell 18, 2919-2928 (2006).
32 Kranz, H. D. et al. Towards functional characterisation of the members of theR2R3-MYBgene family fromArabidopsis thaliana. Plant Journal 16, 263-276 (2010).
33 Moreno, A. A. et al. IRE1/bZIP60-Mediated Unfolded Protein Response Plays Distinct Roles in Plant Immunity and Abiotic Stress Responses. PloS one 7, e31944 (2012).
34 Yu, Y. et al. Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC 1 population between Gossypium hirsutum and G. barbadense. BMC genomics 12, 15 (2011).
35 Nie, X. et al. Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC genomics 17, 352 (2016).
36 Liu, Q. et al. Genetic diversity and population structure of pear (Pyrus spp.) collections revealed by a set of core genome-wide SSR markers. Tree genetics 11, 128 (2015).
37 Khan, M. K. et al. Genome wide SSR high density genetic map construction from an interspecific cross of Gossypium hirsutum× Gossypium tomentosum. Frontiers in plant science 7, 436 (2016).
38 Robertson, K. R., Phipps, J. B. & Smith, R. A Synopsis of Genera in Maloideae (Rosaceae). Systematic Botany 16, 376 (1991).
39 Lei, Z. L. C. H. Z. & Dekui, Z. Pollen Morphology and Cultivar Classification of the Genus Chaenomeles [J]. Scientia Silvae Sinicae 5 (2008).
40 Shao, W. & Jiang, J. The complete chloroplast genome sequences of two Chaenomeles species (Chaenomeles cathayensis and Chaenomeles thibetica). Mitochondrial DNA Part B 5, 3191-3192 (2020).
41 Eckert, C. G., Samis, K. E. & Lougheed, S. C. Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond. Molecular Ecology 17, 1170-1188 (2010).
42 Bartish, I. V., Rumpunen, K. & Nybom, H. Genetic diversity in Chaenomeles (Rosaceae) revealed by RAPD analysis. Plant Systematics & Evolution 214, 131-145 (1999).
43 Duarte, J. M. et al. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryzaand their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 10, 61 (2010).
44 Feau, N., Decourcelle, T., Husson, C., Desprez-Loustau, M.-L. & Dutech, C. Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi. PLoS One 6 (2011).
45 Li, Z. et al. Single-copy genes as molecular markers for phylogenomic studies in seed plants. Genome Biology Evolution 9, 1130-1147 (2017).
46 Teasdale, L. C., Köhler, F., Murray, K. D., O'hara, T. & Moussalli, A. Identification and qualification of 500 nuclear, single‐copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture. Molecular ecology resources 16, 1107-1123 (2016).
47 Wu, F., Mueller, L. A., Crouzillat, D., Pétiard, V. & Tanksley, S. D. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174, 1407-1420 (2006).
48 Cabrera, A. et al. Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers. BMC Genomics 10, 562 (2009).
49 Fan, X. et al. Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase. BMC Evolutionary Biology 9, 247 (2009).
50 Salas-Leiva, D. E. et al. Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods. Annals of Botany 112, 1263-1278 (2013).
51 Han, F., Peng, Y., Xu, L. & Xiao, P. Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes. BMC genomics 15, 504 (2014).
52 Wang, J. S., Jun-Hu, H. E., Chen, H. R., Chen, Y. Y. & University, P. Comparison on the Detection Efficiency of Different Types of Molecular Markers in Pineapple. Hubei Agricultural Sciences (2015).
53 Owczarek, K. et al. Flavanols from Japanese quince (Chaenomeles japonica) fruit suppress expression of cyclooxygenase-2, metalloproteinase-9, and nuclear factor-kappaB in human colon cancer cells. Acta Biochimica Polonica 64, 567–576-567–576 (2017).
54 Zhang, M., Mo, H., Sun, W., Guo, Y. & Li, J. Systematic isolation and characterization of cadmium tolerant genes in tobacco: A cDNA library construction and screening approach. PLoS One 11, e0161147 (2016).
55 Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, 884-890 (2018).
56 Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29, 644 (2011).
57 Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 1-16 (2011).
58 Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Research 12, 656-664 (2002).
59 Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676 (2005).
60 Li, H. et al. MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation. Plant Cell Reports 39, 1199-1217 (2020).
61 Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nature methods 12, 59-60 (2015).
62 Li, L., Stoeckert, C. J. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome research 13, 2178-2189 (2003).
63 Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular biology and evolution 32, 268-274 (2015).
64 Retief, J. D. Phylogenetic analysis using PHYLIP. Methods Mol Biol 132, 243-258 (2000).
65 Wang, D., Zhang, Y., Zhang, Z., Zhu, J. & Yu, J. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics, proteomics bioinformatics 8, 77-80 (2010).
66 Team, A. C. Adobe Illustrator CS5 Classroom in a Book: ADOBE ILLUST CS5 CLASSROOM_p1. (Pearson Education, 2010).
67 Chen, C., Chen, H., He, Y. & Xia, R. TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface. BioRxiv, 289660 (2018).
68 Beier, S., Thiel, T., Münch, T., Scholz, U. & Mascher, M. MISA-web: a web server for microsatellite prediction. Bioinformatics 33, 2583-2585 (2017).
69 Untergasser, A. et al. Primer3—new capabilities and interfaces. Nucleic acids research 40, e115-e115 (2012).
70 Bartish, I., Garkava, L., Rumpunen, K. & Nybom, H. Phylogenetic relationships and differentiation among and within populations of Chaenomeles Lindl.(Rosaceae) estimated with RAPDs and isozymes. Theoretical and Applied Genetics 101, 554-563 (2000).