Genome-wide identififi cation and expression analysis of the frigida domain gene family in Prunus mume (Prunus mume Sieb. et Zucc.)

다국어 초록 (Multilingual Abstract)

Frigida genes play a key role in regulating fl owering time in plants. In this study, we identifi ed 12 PmFRL genes and namedthem according to their chromosomal positions. These genes are unevenly distributed on fi ve chromosomes. Phylogeneticanalysis of Frigida-like proteins of four Rosaceae species and Arabidopsis thaliana showed that these proteins could bedivided into fi ve subfamilies (I–V), and subfamily I ( FRI ) was absent in Rosaceae species. To further reveal the potentialfunctions of these proteins, we performed duplication analysis and found three tandem duplication events and one segmentalduplication event. Tandem duplication promoted the expansion and evolution of the PmFRL genes. RNA-seq analysis showedthat the PmFRL genes were expressed in diff erent tissues, but there were signifi cant diff erences in the expression of somegenes during dormancy. RT-qPCR results supported the RNA-seq results, suggesting that PmFRL genes may be involvedin the regulation of dormancy in Japanese apricot. In conclusion, our comprehensive analysis provides information on theevolution and possible functions of PmFRL genes, laying a foundation for further research on the PmFRL family.

참고문헌 (Reference)

1 Qixiang Zhang, "The genome of Prunus mume" Springer Science and Business Media LLC 3 (3): 1318-, 2012

2 Richard C. Moore, "The early stages of duplicate gene evolution" Proceedings of the National Academy of Sciences 100 (100): 15682-15687, 2003

3 Chen C, "TBtools - an integrative toolkit developed for interactive analyses of big biological data" 2020

4 Kyung-gi Hyun, "Structural Analysis of FRIGIDA Flowering-Time Regulator" Elsevier BV 9 (9): 618-620, 2016

5 Fabio Fornara, "SnapShot: Control of Flowering in Arabidopsis" Elsevier BV 141 (141): 550-550.e2, 2010

6 Zhaoguo Tong, "Selection of reliable reference genes for gene expression studies in peach using real-time PCR" Springer Science and Business Media LLC 10 (10): 71-84, 2009

7 Sanghee Kim, "SUPPRESSOR OF FRIGIDA4, Encoding a C2H2-Type Zinc Finger Protein, Represses Flowering by Transcriptional Activation ofArabidopsis FLOWERING LOCUS C" Oxford University Press (OUP) 18 (18): 2985-2998, 2006

8 Chikako Shindo, "Role of FRIGIDA and FLOWERING LOCUS C in Determining Variation in Flowering Time of Arabidopsis" Oxford University Press (OUP) 138 (138): 1163-1173, 2005

9 Xiangyang Hu, "Proteasome-Mediated Degradation of FRIGIDA Modulates Flowering Time in Arabidopsis during Vernalization" Oxford University Press (OUP) 26 (26): 4763-4781, 2014

10 S. N. Liu, "Overexpression of the repressor gene PvFRI-L from Phyllostachys violascens delays flowering time in transgenic Arabidopsis thaliana" Institute of Experimental Botany 60 (60): 401-409, 2016

11 Julie D. Thompson, "Multiple Sequence Alignment Using ClustalW and ClustalX" Wiley 00 (00): 2-3, 2003

12 Sudhir Kumar, "MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets" Oxford University Press (OUP) 33 (33): 1870-1874, 2016

13 Stephen R Keller, "Local Selection Across a Latitudinal Gradient Shapes Nucleotide Diversity in Balsam Poplar, Populus balsamifera L" Oxford University Press (OUP) 188 (188): 941-952, 2011

14 Isabel C. Bezerra, "Lesions in the mRNA cap-binding gene ABA HYPERSENSITIVE 1 suppress FRIGIDA-mediated delayed flowering in Arabidopsis" Wiley 40 (40): 112-119, 2004

15 Shahid Iqbal, "Identification and expression profiling of sugar transporter genes during sugar accumulation at different stages of fruit development in apricot" Elsevier BV 742 : 144584-, 2020

16 Yanyan Wang, "Identification and characterization of the bZIP transcription factor family and its expression in response to abiotic stresses in sesame" Public Library of Science (PLoS) 13 (13): e0200850-, 2018

17 Lei Wang, "Hydrogen cyanamide improves endodormancy release and blooming associated with endogenous hormones in ‘Summit’ sweet cherry trees" Informa UK Limited 45 (45): 1-15, 2017

18 Natalia Gomes Vieira, "Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica" Springer Science and Business Media LLC 9 (9): 8446-, 2019

19 Liming Miao, "Genome-wide identification, phylogeny, evolution, and expression patterns of MtN3/saliva/SWEET genes and functional analysis of BcNS in Brassica rapa" Springer Science and Business Media LLC 19 (19): 174-, 2018

20 Lulu Li, "Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume" PeerJ 7 : e7499-, 2019

21 Jian Ma, "Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.)" Public Library of Science (PLoS) 12 (12): e0181443-, 2017

22 Yanbing G, "Genome-wide identifi cation and expression analysis of the WRKY gene family in peach" 38 : 254-270, 2016

23 Li J, "Genome-wide identifi cation and analysis of the SBP-box family genes in apple(Malus×domesticaBorkh. )" 70 : 100-114, 2013

24 Wenjun Zhong, "Genome-wide expression profiles of seasonal bud dormancy at four critical stages in Japanese apricot" Springer Science and Business Media LLC 83 (83): 247-264, 2013

25 Yujiao Wang, "Genome-wide analysis of VQ motif-containing proteins in Moso bamboo (Phyllostachys edulis)" Springer Science and Business Media LLC 246 (246): 165-181, 2017

26 Zhenjun Li, "Genome-Wide Identification and Analysis of the MYB Transcription Factor Superfamily inSolanum lycopersicum" Oxford University Press (OUP) 57 (57): 1657-1677, 2016

27 Feng Cheng, "Gene retention, fractionation and subgenome differences in polyploid plants" Springer Science and Business Media LLC 4 (4): 258-268, 2018

28 Zhang L, "Functional analysis of FRIGIDA using naturally occurring variation in Arabidopsis thaliana" 2020

29 S. D. Michaels, "FRIGIDA-related genes are required for the winter-annual habit in Arabidopsis" Proceedings of the National Academy of Sciences 101 (101): 3281-3285, 2004

30 Robert J. Schmitz, "FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDAand FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana" The Company of Biologists 132 (132): 5471-5478, 2005

31 Zicong Li, "FRIGIDA establishes a local chromosomal environment for FLOWERING LOCUS C mRNA production" Springer Science and Business Media LLC 4 (4): 836-846, 2018

32 Joanna M. Risk, "FRIGIDA and related proteins have a conserved central domain and family specific N- and C- terminal regions that are functionally important" Springer Science and Business Media LLC 73 (73): 493-505, 2010

33 Schläppi MR, "FRIGIDA LIKE 2 is a functional allele in Landsberg erecta and compensates for a nonsense allele of FRIGIDA LIKE 1" 142 : 1728-1738, 2007

34 Yuehui Chao, "Expression of the alfalfa FRIGIDA-Like Gene, MsFRI-L delays flowering time in transgenic Arabidopsis thaliana" Springer Science and Business Media LLC 40 (40): 2083-2090, 2013

35 Gao Z, "Evaluation of chilling and heat requirements in japanese apricot with three models" 47 : 1826-1831, 2012

36 Guixia Xu, "Divergence of duplicate genes in exon–intron structure" Proceedings of the National Academy of Sciences 109 (109): 1187-1192, 2012

37 B. G. Hall, "Building Phylogenetic Trees from Molecular Data with MEGA" Oxford University Press (OUP) 30 (30): 1229-1235, 2013

38 Shi T, "Association between blooming time and climatic adaptation in Prunus mume" 2020

39 Stephen A. Goff, "A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)" American Association for the Advancement of Science (AAAS) 296 (296): 92-100, 2002