[1] Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F. 2018. Trends in plant research using molecular markers. Planta 247:543−57 doi: 10.1007/s00425-017-2829-y
[2] Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK. 2011. Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309−34 doi: 10.1007/s10681-010-0286-9
[3] Varshney RK, Graner A, Sorrells ME. 2005. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology 23:48−55 doi: 10.1016/j.tibtech.2004.11.005
[4] Vieira ML, Santini L, Diniz AL, Munhoz Cde F. 2016. Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology 39:312−28 doi: 10.1590/1678-4685-GMB-2016-0027
[5] Ranade SS, Lin YC, Van de Peer Y, García-Gil MR. 2015. Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda). BMC Genetics 16:149 https://bmcgenomdata.biomedcentral.com/articles/10.1186/s12863-015-0304-y
[6] Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellite isolation: a review. Molecular ecology 11:1−16 doi: 10.1046/j.0962-1083.2001.01418.x
[7] Mayer C, Leese F, Tollrian R. 2010. Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC Genomics 11:277 doi: 10.1186/1471-2164-11-277
[8] da Maia LC, de Souza VQ, Kopp MM, de Carvalho FI, de Oliveira AC. 2009. Tandem repeat distribution of gene transcripts in three plant families. Genetics and Molecular Biology 32:822−33 doi: 10.1590/S1415-47572009005000091
[9] von Stackelberg M, Rensing SA, Reski R. 2006. Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. BMC Plant Biology 6:9 doi: 10.1186/1471-2229-6-9
[10] Xu J, Liu L, Xu Y, Chen C, Rong T, et al. 2013. Development and characterization of simple sequence repeat markers providing genome-wide coverage and high resolution in maize. DNA Research 20:497−509 doi: 10.1093/dnares/dst026
[11] Zhang L, Yuan D, Yu S, Li Z, Cao Y, et al. 2004. Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 20:1081−6 doi: 10.1093/bioinformatics/bth043
[12] Legendre M, Pochet N, Pak T, Verstrepen KJ. 2007. Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research 17:1787−96 doi: 10.1101/gr.6554007
[13] Metzgar D, Liu L, Hansen C, Dybvig K, Wills C. 2002. Domain-level differences in microsatellite distribution and content result from different relative rates of insertion and deletion mutations. Genome Research 12:408−13 doi: 10.1101/gr.198602
[14] Li Y, Korol AB, Fahima T, Beiles A, Nevo E. 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology 11:2453−65 doi: 10.1046/j.1365-294X.2002.01643.x
[15] Nevo E. 2001. Evolution of genome-phenome diversity under environmental stress. PNAS 98:6233−40 doi: 10.1073/pnas.101109298
[16] Gao C, Ren X, Mason AS, Li J, Wang W, et al. 2013. Revisiting an important component of plant genomes: microsatellites. Functional Plant Biology 40:645−61 doi: 10.1071/FP12325
[17] Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, et al. 2012. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. American Journal of Botany 99:193−208 doi: 10.3732/ajb.1100394
[18] Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, et al. 2018. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 23:399 doi: 10.3390/molecules23020399
[19] Šarhanová P, Pfanzelt S, Brandt R, Himmelbach A, Blattner FR. 2018. SSR-seq: Genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring. Ecology and Evolution 8:10817−33 doi: 10.1002/ece3.4533
[20] Biswas MK, Xu Q, Mayer C, Deng X. 2014. Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis). PLoS One 9:e104182 doi: 10.1371/journal.pone.0104182
[21] Liang M, Yang X, Li H, Su S, Yi H, et al. 2015. De novo transcriptome assembly of pummelo and molecular marker development. PLoS One 10:e0120615 doi: 10.1371/journal.pone.0120615
[22] Jia H, Yang H, Sun P, Li J, Zhang J, et al. 2016. De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila. Scientific Reports 6:39591 doi: 10.1038/srep39591
[23] Tian W, Paudel D, Vendrame W, Wang J. 2017. Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies. International Journal of Genomics 2017:8614160 doi: 10.1155/2017/8614160
[24] El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, et al. 2019. The Pfam protein families database in 2019. Nucleic Acids Research 47:D427−D432 doi: 10.1093/nar/gky995
[25] Nagano Y. 2000. Several features of the GT-factor trihelix domain resemble those of the Myb DNA-binding domain. Plant Physiology 124:491−4 doi: 10.1104/pp.124.2.491
[26] Song X, Li Y, Hou X. 2013. Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 14:573 doi: 10.1186/1471-2164-14-573
[27] Liu M, Sun W, Ma Z, Zheng T, Huang L, et al. 2019. Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum). BMC Plant Biology 19:84 doi: 10.1186/s12870-019-1681-6
[28] Zhao Y, Ma R, Xu D, Bi H, Xia Z, Peng H. 2019. Genome-Wide Identification and Analysis of the AP2 Transcription Factor Gene Family in Wheat (Triticum aestivum L.). Frontiers In Plant Science 10:1286 doi: 10.3389/fpls.2019.01286
[29] Aukerman MJ, Sakai H. 2003. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15:2730−41 doi: 10.1105/tpc.016238
[30] Yamamoto T, Terakami S. 2016. Genomics of pear and other Rosaceae fruit trees. Breeding Science 66:148−59 doi: 10.1270/jsbbs.66.148
[31] Carrasco B, Meisel L, Gebauer M, Garcia-Gonzales R, Silva H. 2013. Breeding in peach, cherry and plum: from a tissue culture, genetic, transcriptomic and genomic perspective. Biological Research 46:219−30 doi: 10.4067/S0716-97602013000300001
[32] Sumathi M, Yasodha R. 2014. Microsatellite resources of Eucalyptus: current status and future perspectives. Botanical Studies 55:73 doi: 10.1186/s40529-014-0073-3
[33] Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, et al. 2000. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105−10 doi: 10.1126/science.290.5499.2105
[34] Song X, Wang J, Sun P, Ma X, Yang Q, et al. 2020. Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization. Horticulture Research 7:20 doi: 10.1038/s41438-020-0253-0
[35] Song X, Nie F, Chen W, Ma X, Gong K, et al. 2020. Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander. Horticulture Research 7:55 doi: 10.1038/s41438-020-0261-0
[36] Song X, Liu G, Duan W, Liu T, Huang Z, et al. 2014. Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. Molecular Genetics and Genomics 289:541−51 doi: 10.1007/s00438-014-0833-5
[37] Agarwal PK, Agarwal P, Reddy MK, Sopory SK. 2006. Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Reports 25:1263−74 doi: 10.1007/s00299-006-0204-8
[38] Baillo EH, Kimotho RN, Zhang Z, Xu P. 2019. Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement. Genes (Basel) 10:771 doi: 10.3390/genes10100771
[39] Song X, Sun P, Yuan J, Gong K, Li N, et al. 2020. The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales. Plant Biotechnology Journal doi: 10.1111/pbi.13499
[40] Kaplan-Levy RN, Brewer PB, Quon T, Smyth DR. 2012. The trihelix family of transcription factors − light, stress and development. Trends in Plant Science 17:163−71 doi: 10.1016/j.tplants.2011.12.002
[41] Nagano Y, Inaba T, Furuhashi H, Sasaki Y. 2001. Trihelix DNA-binding protein with specificities for two distinct cis-elements: both important for light down-regulated and dark-inducible gene expression in higher plants. Journal of Biological Chemistry 276:22238−43 doi: 10.1074/jbc.M102474200
[42] Wang Z, Liu Q, Wang H, Zhang H, Xu X, et al. 2016. Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa. Scientific Reports 6:36274 doi: 10.1038/srep36274
[43] Xi J, Qiu Y, Du L, Poovaiah BW. 2012. Plant-specific trihelix transcription factor AtGT2L interacts with calcium/calmodulin and responds to cold and salt stresses. Plant Science 185-186:274−80 doi: 10.1016/j.plantsci.2011.11.013
[44] Fang Y, Xie K, Hou X, Hu H, Xiong L. 2010. Systematic analysis of GT factor family of rice reveals a novel subfamily involved in stress responses. Molecular Genetics and Genomics 283:157−69 doi: 10.1007/s00438-009-0507-x
[45] Brewer PB, Howles PA, Dorian K, Griffith ME, Ishida T, et al. 2004. PETAL LOSS, a trihelix transcription factor gene, regulates perianth architecture in the Arabidopsis flower. Development 131:4035−45 doi: 10.1242/dev.01279
[46] Li J, Zhang M, Sun J, Mao X, Wang J, et al. 2019. Genome-Wide Characterization and Identification of Trihelix Transcription Factor and Expression Profiling in Response to Abiotic Stresses in Rice (Oryza sativa L.). International Journal of Molecular Sciences 20:251 doi: 10.3390/ijms20020251
[47] Yu C, Song L, Song J, Ouyang B, Guo L, et al. 2018. ShCIGT, a Trihelix family gene, mediates cold and drought tolerance by interacting with SnRK1 in tomato. Plant Science 270:140−9 doi: 10.1016/j.plantsci.2018.02.012
[48] Liu W, Zhang Y, Li W, Lin Y, Wang C, et al. 2020. Genome-wide characterization and expression analysis of soybean trihelix gene family. PeerJ 8:e8753 doi: 10.7717/peerj.8753
[49] Xiao J, Hu R, Gu T, Han J, Qiu D, et al. 2019. Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat. BMC Genomics 20:287 doi: 10.1186/s12864-019-5632-2
[50] Licausi F, Ohme-Takagi M, Perata P. 2013. APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. New Phytologist 199:639−49 doi: 10.1111/nph.12291
[51] Li M, Xu Z, Huang Y, Tian C, Wang F, et al. 2015. Genome-wide analysis of AP2/ERF transcription factors in carrot (Daucus carota L.) reveals evolution and expression profiles under abiotic stress. Molecular Genetics and Genomics 290:2049−61 doi: 10.1007/s00438-015-1061-3
[52] Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK. 1994. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6:1211−25 doi: 10.1105/tpc.6.9.1211
[53] Song X, Wang J, Ma X, Li Y, Lei T, et al. 2016. Origination, expansion, evolutionary trajectory, and expression bias of AP2/ERF superfamily in Brassica napus. Frontiers in Plant Science 7:1186 doi: 10.3389/fpls.2016.01186
[54] Irish VF, Sussex IM. 1990. Function of the apetala-1 gene during Arabidopsis floral development. The Plant Cell 2:741−53 doi: 10.1105/tpc.2.8.741
[55] Shannon S, Meeks-Wagner DR. 1993. Genetic Interactions That Regulate Inflorescence Development in Arabidopsis. The Plant Cell 5:639−55 doi: 10.2307/3869807
[56] Sun X, Shantharaj D, Kang X, Ni M. 2010. Transcriptional and hormonal signaling control of Arabidopsis seed development. Current Opinion in Plant Biology 13:611−20 doi: 10.1016/j.pbi.2010.08.009
[57] Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M, et al. 2010. Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. BMC Genomics 11:719 doi: 10.1186/1471-2164-11-719
[58] Zhang C, Shangguan L, Ma R, Sun X, Tao R, et al. 2012. Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica). Genetics and Molecular Research 11:4789−809 doi: 10.4238/2012.October.17.6
[59] Zhuang J, Cai B, Peng R, Zhu B, Jin X, et al. 2008. Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochemical and Biophysical Research Communications 371:468−74 doi: 10.1016/j.bbrc.2008.04.087
[60] Das Laha S, Dutta S, Schäffner AR, Das M. 2020. Gene duplication and stress genomics in Brassicas: Current understanding and future prospects. Journal of Plant Physiology 255:153293 doi: 10.1016/j.jplph.2020.153293
[61] Schranz ME, Mohammadin S, Edger PP. 2012. Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. Current Opinion in Plant Biology 15:147−53 doi: 10.1016/j.pbi.2012.03.011
[62] Soltis PS, Soltis DE. 2016. Ancient WGD events as drivers of key innovations in angiosperms. Current Opinion in Plant Biology 30:159−65 doi: 10.1016/j.pbi.2016.03.015
[63] Beier S, Thiel T, Munch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−5 doi: 10.1093/bioinformatics/btx198
[64] Song X, Ge T, Li Y, Hou X. 2015. Genome-wide identification of SSR and SNP markers from the non-heading Chinese cabbage for comparative genomic analyses. BMC Genomics 16:328 doi: 10.1186/s12864-015-1534-0
[65] Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics Methods and Protocols, Methods in Molecular Biology™, eds. Misener S, Krawetz SA. vol 132. Totowa, NJ: Humana Press. pp. 365−86 https://doi.org/10.1385/1-59259-192-2:365
[66] Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, et al. 2020. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods 17:261−72 doi: 10.1038/s41592-019-0686-2
[67] Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Molecular Plant 13:1194−202 doi: 10.1016/j.molp.2020.06.009
[68] Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, et al. 2014. Pfam: the protein families database. Nucleic Acids Res 42:D222−D230 doi: 10.1093/nar/gkt1223
[69] Letunic I, Doerks T, Bork P. 2012. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Research 40:D302−D305 doi: 10.1093/nar/gkr931
[70] Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, Deweese-Scott C, et al. 2009. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Research 37:D205−D210 doi: 10.1093/nar/gkn845
[71] Song X, Liu T, Duan W, Ma Q, Ren J, et al. 2014. Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis). Genomics 103:135−46 doi: 10.1016/j.ygeno.2013.12.004
[72] Nakamura T, Yamada KD, Tomii K, Katoh K. 2018. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 34:2490−2 doi: 10.1093/bioinformatics/bty121
[73] Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution 26:1641−50 doi: 10.1093/molbev/msp077
[74] Letunic I, Bork P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research 47:W256−W259 doi: 10.1093/nar/gkz239
[75] Stolzer M, Lai H, Xu M, Sathaye D, Vernot B, et al. 2012. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28:i409−i415 doi: 10.1093/bioinformatics/bts386
[76] Wang T, Hu J, Ma X, Li C, Yang Q, et al. 2020. Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus. BMC Genomics 21:264 doi: 10.1186/s12864-020-6678-x
[77] Song X, Ma X, Li C, Hu J, Yang Q, et al. 2018. Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species. BMC Genomics 19:346 doi: 10.1186/s12864-018-4744-4