Xác định toàn bộ bộ gen và phân tích phiên mã của gia đình gen TCP ở chuối (Musa acuminata L.)

Biochemical Genetics - Tập 60 - Trang 204-222 - 2021
Jingyi Wang1, Zhuo Wang1,2, Caihong Jia1, Hongxia Miao1,2, Jianbin Zhang1, Juhua Liu1,2, Biyu Xu1, Zhiqiang Jin1,2
1Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
2Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China

Tóm tắt

Gia đình gen TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) ở thực vật có nhiều chức năng đa dạng trong nhiều khía cạnh của thực vật. Tuy nhiên, nghiên cứu về các gen TCP ở chuối vẫn chưa được thực hiện một cách toàn diện. Vì vậy, 48 gen TCP ở chuối đã được đặc trưng trên các khía cạnh của cấu trúc gen, động cơ bảo tồn, mối quan hệ phát sinh chủng loài và các kiểu hình biểu hiện. Các thành viên trong gia đình gen MaTCP phân bố không đồng đều trên 11 nhiễm sắc thể và chọn lọc tinh lọc là động lực chính của gia đình gen MaTCP. Phân tích sự sao chép gen cho thấy rằng sự sao chép đoạn là nguyên nhân chính góp phần vào sự mở rộng của gia đình. Phân tích trình tự promoter cho thấy rằng các gen MaTCP có thể tham gia vào sự phát triển, tăng trưởng cây chuối và phản ứng của cây trước áp lực môi trường. Hơn nữa, sự biểu hiện của 12 gen MaTCP đã được phân tích bằng RT-PCR định lượng thời gian thực, và phân tích tương tác protein cho thấy MaPCF10 và MaPCF13 có thể đóng vai trò quan trọng trong sự phát triển và chín của trái chuối. Những kết quả này tạo nền tảng cho việc nghiên cứu chức năng của các gen TCP ở chuối.

Từ khóa

#gen TCP #chuối #Musa acuminata #phân tích phiên mã #phát sinh chủng loài #biểu hiện gen

Tài liệu tham khảo

Aguilar-Martínez JA, Poza-Carrión C, Cubas P (2007) Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds. Plant Cell 19(2):458–472. https://doi.org/10.1105/tpc.106.048934 Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815. https://doi.org/10.1038/35048692 Bao S, Zhang Z, Lian Q, Sun Q, Zhang R (2019) Evolution and expression of genes encoding TCP transcription factors in Solanum tuberosum reveal the involvement of StTCP23 in plant defence. BMC Genet 20:91. https://doi.org/10.1186/s12863-019-0793-1 Chai W, Jiang P, Huang G, Jiang H, Li X (2017) Identification and expression profiling analysis of TCP family genes involved in growth and development in maize. Physiol Mol Biol Plants 23(4):779–791. https://doi.org/10.1007/s12298-017-0476-1 Cubas P, Lauter N, Doebley J, Coen E (1999) The TCP domain: a motif found in proteins regulating plant growth and development. Plant J 18(2):215–222. https://doi.org/10.1046/j.1365-313x.1999.00444.x Dai X, Zhao P (2011) psRNATarget: A plant small RNA target analysis server. Nucleic Acids Res. 39:W155–W159. https://doi.org/10.1093/nar/gkr319.P D’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217. https://doi.org/10.1038/nature11241 Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386(6624):485–488. https://doi.org/10.1038/386485a0 Giraud E, Ng S, Carrie C, Duncan O, Low J, Lee CP, Van Aken O, Millar AH, Murcha M, Whelan J (2010) TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana. Plant Cell 22(12):3921–3934. https://doi.org/10.1105/tpc.110.074518 Goel R, Pandey A, Trivedi PK, Asif MH (2016) Genome-wide analysis of the Musa WRKY gene family: evolution and differential expression during development and stress. Front Plant Sci 7:299. https://doi.org/10.3389/fpls.2016.00299 Guo R, Xu X, Carole B, Li X, Gao M, Zheng Y, Wang X (2013) Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape. BMC Genom 14:554. https://doi.org/10.1186/1471-2164-14-554 Hammani K, Gobert A, Hleibieh K, Choulier L, Small I, Giegé P (2011) An Arabidopsis dual-localized pentatricopeptide repeat protein interacts with nuclear proteins involved in gene expression regulation. Plant Cell 23(2):730–740. https://doi.org/10.1105/tpc.110.081638 Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G (2015a) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31(8):1296–1297. https://doi.org/10.1093/bioinformatics/btu817 Hu W, Zuo J, Hou X, Yan Y, Wei Y, Liu J, Li M, Xu B, Jin Z (2015b) The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress. Front Plant Sci 6:742. https://doi.org/10.3389/fpls.2015.00742 Kieffer M, Master V, Waites R, Davies B (2011) TCP14 and TCP15 affect internode length and leaf shape in Arabidopsis. Plant J 68(1):147–158. https://doi.org/10.1111/j.1365-313X.2011.04674.x Kosugi S, Ohashi Y (2002) DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J 30(3):337–348. https://doi.org/10.1046/j.1365-313x.2002.01294.x Lakhwani D, Pandey A, Dhar YV, Bag SK, Trivedi PK, Asif MH (2016) Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution. Sci Rep 6:18878. https://doi.org/10.1038/srep18878 Leister D (2004) Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes. Trends Genet 20(3):116–122. https://doi.org/10.1016/j.tig.2004.01.007 Lei N, Yu X, Li S, Zeng C, Zou L, Liao W, Peng M (2017) Phylogeny and expression pattern analysis of TCP transcription factors in cassava seedlings exposed to cold and/or drought stress. Sci Rep 7:10016. https://doi.org/10.1038/s41598-017-09398-5 Leng X, Wei H, Xu X, Ghuge SA, Jia D, Liu G, Wang Y, Yuan Y (2019) Genome-wide identification and transcript analysis of TCP transcription factors in grapevine. BMC Genom 20(1):786. https://doi.org/10.1186/s12864-019-6159-2 Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30(1):325–327. https://doi.org/10.1093/nar/30.1.325 Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CM, D’Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ Jr, Sasaki T, Souza MT Jr, Miller RN, Glaszmann JC, Town CD (2008) Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 9:58. https://doi.org/10.1186/1471-2164-9-58 Li S (2015) The Arabidopsis thaliana TCP transcription factors: a broadening horizon beyond development. Plant Signal Behav 10(7):e1044192. https://doi.org/10.1080/15592324.2015.1044192 Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452. https://doi.org/10.1093/bioinformatics/btp187 Liu Y, Guan X, Liu S, Yang M, Ren J, Guo M, Huang Z, Zhang Y (2018) Genome-wide identification and analysis of TCP transcription factors involved in the formation of leafy head in Chinese cabbage. Int J Mol Sci 19(3):847. https://doi.org/10.3390/ijms19030847 Liu MM, Wang MM, Yang J, Wen J, Guo PC, Wu YW, Ke YZ, Li PF, Li JN, Du H (2019) Evolutionary and comparative expression analyses of TCP transcription factor gene family in land plants. Int J Mol Sci 20(14):3591. https://doi.org/10.3390/ijms20143591 Livark KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−△△CT method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262 Luo D, Carpenter R, Copsey L, Vincent C, Clark J, Coen E (1999) Control of organ asymmetry in flowers of Antirrhinum. Cell 99(4):367–376. https://doi.org/10.1016/s0092-8674(00)81523-8 Ma J, Wang Q, Sun R, Xie F, Jones DC, Zhang B (2014) Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii. Sci Rep 4:6645. https://doi.org/10.1038/srep06645 Manassero NG, Viola IL, Welchen E, Gonzalez DH (2013) TCP transcription factors: architectures of plant form. Biomol Concepts 4(2):111–127. https://doi.org/10.1515/bmc-2012-0051 Martín-Trillo M, Cubas P (2010) TCP genes: a family snapshot ten years later. Trends Plant Sci 15(1):31–39. https://doi.org/10.1016/j.tplants.2009.11.003 Martin G, Baurens FC, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Dolezel J, Aury JM, Alberti A, Carreel F, D’Hont A (2016) Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatic methods. BMC Genom 17:243. https://doi.org/10.1186/s12864-016-2579-4 Masuda HP, Cabral LM, De Veylder L, Tanurdzic M, de Almeida EJ, Geelen D, Inzé D, Martienssen RA, Ferreira PC, Hemerly AS (2008) ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription. EMBO J 27(20):2746–2756. https://doi.org/10.1038/emboj.2008.191 Mattick JS, Gagen MJ (2001) The evolution of controlled multitasked gene networks: the introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 18(9):1611–1630. https://doi.org/10.1093/oxfordjournals.molbev.a003951 Ori N, Cohen AR, Etzioni A, Brand A, Yanai O, Shleizer S, Menda N, Amsellem Z, Efroni I, Pekker I, Alvarez JP, Blum E, Zamir D, Eshed Y (2007) Regulation of LANCEOLATE by miR319 is required for compound- leaf development in tomato. Nat Genet 39(6):787–791. https://doi.org/10.1038/ng2036 Pagnussat GC, Yu HJ, Ngo QA, Rajani S, Mayalagu S, Johnson CS, Capron A, Xie LF, Ye D, Sundaresan V (2005) Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development 132(3):603–614. https://doi.org/10.1242/dev.01595 Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D (2003) Control of leaf morphogenesis by microRNAs. Nature 425(6955):257–263. https://doi.org/10.1038/nature01958 Parapunova V, Busscher M, Busscher-Lange J, Lammers M, Karlova R, Bovy AG, Angenent GC, de Maagd RA (2014) Identification, cloning and characterization of the tomato TCP transcription factor family. BMC Plant Biol 14:157. https://doi.org/10.1186/1471-2229-14-157 Pillet J, Yu HW, Chambers AH, Whitaker VM, Folta KM (2015) Identification of candidate flavonoid pathway genes using transcriptome correlation network analysis in ripe strawberry (Fragaria × ananassa) fruits. J Exp Bot 66(15):4455–4467. https://doi.org/10.1093/jxb/erv205 Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290(5499):2105–2110. https://doi.org/10.1126/science.290.5499.2105 Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci 95(11):5857–5864. https://doi.org/10.1073/pnas.95.11.5857 Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504. https://doi.org/10.1101/gr.1239303 Song CB, Shan W, Yang YY, Tan XL, Fan ZQ, Chen JY, Lu WJ, Kuang JF (2018) Heterodimerization of MaTCP proteins modulates the transcription of MaXTH10/11 genes during banana fruit ripening. Biochim Biophys Acta Gene Regul Mech 1861(7):613–622. https://doi.org/10.1016/j.bbagrm.2018.06.005 Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M, Matsuoka M, Ueguchi C (2003) The OsTB1 gene negatively regulates lateral branching in rice. Plant J 33(3):513–520. https://doi.org/10.1046/j.1365-313x.2003.01648.x Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. https://doi.org/10.1093/molbev/msr121 Tatematsu K, Nakabayashi K, Kamiya Y, Nambara E (2008) Transcription factor AtTCP14 regulates embryonic growth potential during seed germination in Arabidopsis thaliana. Plant J 53(1):42–52. https://doi.org/10.1111/j.1365-313X.2007.03308.x Wang Z, Jia C, Wang JY, Miao HX, Liu JH, Chen C, Yang HX, Xu B, Jin Z (2020) Genome-Wide Analysis of Basic Helix-Loop-Helix Transcription Factors to Elucidate Candidate Genes Related to Fruit Ripening and Stress in Banana (Musa acuminata L. AAA Group, cv. Cavendish). Front Plant Sci 11:650. https://doi.org/10.3389/fpls.2020.00650 Wei W, Hu Y, Cui MY, Han YT, Gao K, Feng JY (2016) Identification and transcript analysis of the TCP transcription factors in the diploid woodland strawberry Fragaria vesca. Front Plant Sci 7:1937. https://doi.org/10.3389/fpls.2016.01937 Xu R, Sun P, Jia F, Lu L, Li Y, Zhang S, Huang J (2014) Genome wide analysis of TCP transcription factor gene family in Malus domestica. J Genet 93(3):733–746. https://doi.org/10.1007/s12041-014-0446-0 Yang S, Zhang X, Yue JX, Tian D, Chen JQ (2008) Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genom 280(3):187–198. https://doi.org/10.1007/s00438-008-0355-0 Yao X, Ma H, Wang J, Zhang D (2007) Genome-wide comparative analysis and expression pattern of TCP gene families in Arabidopsis thaliana and Oryza sativa. J Integr Plant Biol 49(6):885–897. https://doi.org/10.1111/j.1744-7909.2007.00509.x Zhao J, Zhai Z, Li Y, Geng S, Song G, Guan J, Jia M, Wang F, Sun G, Feng N, Kong X, Chen L, Mao L, Li A (2018) Genome-wide identification and expression profiling of the TCP family genes in spike and grain development of wheat (Triticum aestivum L.). Front in Plant Sci 9:1282. https://doi.org/10.3389/fpls.2018.01282 Zhou Y, Xu Z, Zhao K, Yang W, Cheng T, Wang J, Zhang Q (2016) Genome-wide identification, characterization and expression analysis of the TCP gene family in Prunus mume. Front Plant Sci 7:1301. https://doi.org/10.3389/fpls.2016.01301