西瓜 TALE 基因家族鉴定及表达分析

Identification and expression analysis of TALE gene family in watermelon

摘要

TALE 基因家族在调控花器官发育、花分生组织形成、器官形态发生、果实发育、植物非生物胁迫响应及激素响应中发挥重要作用。利用生物信息学的方法鉴定了西瓜 TALE 基因家族成员，并分析了其基因结构、系统发育树、保守基序、顺式作用元件、组织特异性表达，以及低温胁迫和干旱胁迫后基因的表达情况，为西瓜 TALE 基因家族的功能研究和利用提供了理论依据。结果表明，西瓜 TALE 基因家族共包含 19 个成员。系统发育分析将 ClTALE 家族分为 BEL1-like 和 KNOX 两个亚家族，KNOX 亚家族又可进一步划分为两个分支 Class I 和 Class II。顺式作用元件分析表明， ClTALE 基因的启动子中富含光、植物激素和非生物胁迫响应的顺式元件，其中光响应元件最多。西瓜组织特异性表达分析表明， ClBLH09 在根中高表达， ClBLH01 在卷须、雌花和雄花中高表达，因此西瓜 TALE 基因家族可能参与了西瓜的生长发育过程。低温胁迫(0、3、6、12、24、36 和 48 h)和干旱胁迫(0、1、2、3、4、5、6、7 和 8 d)不同时间后基因的表达分析表明， ClBLH08 和 ClKN02 在低温胁迫下呈现上调趋势， ClBLH04 和 ClBLH05 在干旱胁迫下呈上调的趋势，因此西瓜 TALE 基因家族可能在低温胁迫和干旱胁迫中发挥作用。

Abstract

The TALE gene family plays a pivotal role in regulating various aspects of plant growth and development, including floral organ development, floral meristem formation, organ morphogenesis, and fruit development, as well as mediating plant responses to abiotic stress and hormone signals. This study utilized bioinformatics methods to identify members of the TALE gene family in watermelon and conducted a comprehensive analysis of their gene structure, phylogenetic relationships, conserved motifs, cis-acting elements, tissue-specific expression patterns, and gene expression profiles under low temperature and drought stress conditions. This analysis provides a theoretical foundation for further functional studies and utilization of the TALE gene family in watermelon. The results revealed that the watermelon TALE gene family consists of a total of 19 members. Phylogenetic analysis classified the ClTALE family into two distinct subfamilies: BEL1-like and KNOX, with the KNOX subfamily further subdivided into two classes, Class I and Class II. Cis-acting element analysis demonstrated that the promoters of ClTALE genes are enriched in cis-elements that respond to light, plant hormones, and abiotic stresses, with light-responsive elements being the most prevalent. Tissue-specific expression analysis in watermelon indicated that ClBLH09 is highly expressed in roots, while ClBLH01 exhibits high expression levels in tendrils, female flowers, and male flowers, implying that the watermelon TALE gene family may be involved in the growth and development of watermelon. Gene expression analysis at various time points under low temperature stress (0, 3, 6, 12, 24, 36, and 48 h) and drought stress (0, 1, 2, 3, 4, 5, 6, 7, and 8 d) revealed that ClBLH08 and ClKN02 exhibited an upward trend in expression under low temperature stress, while ClBLH04 and ClBLH05 showed an upward trend under drought stress. These findings suggested that the watermelon TALE gene family may play a significant role in mediating responses to low temperature and drought stress.

关键词

西瓜 / TALE 基因家族 / 生物信息学 / 表达分析

Key words

Watermelon / TALE gene family / Bioinformatics / Expression analysis

参考文献

[1] BÜRGLIN T R, AFFOLTER M. Homeodomain proteins: An update[J]. Chromosoma, 2016, 125(3): 497-521.

[2] ARNAUD N, PAUTOT V. Ring the BELL and tie the KNOX: Roles for TALEs in gynoecium development[J]. Frontiers in Plant Science, 2014, 5: 93.

[3] MA Q, WANG N H, HAO P B, et al. Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis[J]. BMC Plant Biology, 2019, 19(1): 432.

[4] CHEN H, ROSIN F M, PRAT S, et al. Interacting transcription factors from the three-amino acid loop extension superclass regulate tuber formation[J]. Plant Physiology, 2003, 132(3): 1391-1404.

[5] HAY A, TSIANTIS M. KNOX genes: Versatile regulators of plant development and diversity[J]. Development, 2010, 137(19): 3153-3165.

[6] BERTOLINO E, REIMUND B, WILDTPERINIC D, et al. A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif[J]. Journal of Biological Chemistry, 1995, 270(52): 31178-31188.

[7] MAHAJAN A, BHOGALE S, KANG I H, et al. The mRNA of a Knotted1-like transcription factor of potato is phloem mobile[J]. Plant Molecular Biology, 2012, 79(6): 595-608.

[8] SAKAKIBARA K, ANDO S, YIP H K, et al. KNOX2 genes regulate the haploid-to-diploid morphological transition in land plants[J]. Science, 2013, 339(6123): 1067-1070.

[9] LIN T, SHARMA P, GONZALEZ D H, et al. The impact of the long-distance transport of a BEL1-Like Messenger RNA on development[J]. Plant Physiology, 2013, 161(2): 760-772.

[10] FURUMIZU C, ALVAREZ J P, SAKAKIBARA K, et al. Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication[J]. PLoS Genetics, 2015, 11(2): e1004980.

[11] RUIZ-ESTÉVEZ M, BAKKALI M, MARTIN-BLAZQUEZ R, et al. Identification and characterization of TALE homeobox genes in the endangered fern Vandenboschia speciosa[J]. Genes, 2017, 8(10): 275.

[12] BELLES-BOIX E, HAMANT O, WITIAK S M, et al. KNAT6: An Arabidopsis homeobox gene involved in meristem activity and organ separation[J]. Plant Cell, 2006, 18(8): 1900-1907.

[13] AIDA M, ISHIDA T, TASAKA M. Shoot apical meristem and cotyledon formation during Arabidopsis embryogenesis: Interaction among the CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS genes[J]. Development, 1999, 126(8): 1563-1570.

[14] SHANI E, YANAI O, ORI N. The role of hormones in shoot apical meristem function[J]. Current Opinion in Plant Biology, 2006, 9(5): 484-489.

[15] CNOPS G, NEYT P, RAES J, et al. The TORNADO1 and TORNADO2 genes function in several patterning processes during early leaf development in Arabidopsis thaliana[J]. Plant Cell, 2006, 18(4): 852-866.

[16] KONDHARE K R, VETAL P V, KALSI H S, et al. BEL1-like protein (StBEL5) regulates CYCLING DOF FACTOR1 (StCDF1) through tandem TGAC core motifs in potato[J]. Journal of Plant Physiology, 2019, 241: 153014.

[17] BHATT A M, ETCHELLS J P, CANALES C, et al. Vaamana-a BEL1-like homeodomain protein, interacts with KNOX proteins BP and STM and regulates inflorescence stem growth in Arabidopsis[J]. Gene, 2004, 328: 103-111.

[18] KIM D, CHO Y H, RYU H, et al. BLH1 and KNAT3 modulate ABA responses during germination and early seedling development in Arabidopsis[J]. Plant Journal, 2013, 75(5): 755-766.

[19] SMITH H M S, BOSCHKE I, HAKE S. Selective interaction of plant homeodomain proteins mediates high DNA-binding affinity[J]. Proceedings of the National Academy of Sciences of the United States of America, 2002, 99(14): 9579-9584.

[20] BYRNE M E, GROOVER A T, FONTANA J R, et al. Phyllotactic pattern and stem cell fate are determined by the Arabidopsis homeobox gene BELLRINGER[J]. Development, 2003, 130(17): 3941-3950.

[21] MENG L H, FAN Z Q, ZHANG Q, et al. BEL1-LIKE HOMEODOMAIN 11 regulates chloroplast development and chlorophyll synthesis in tomato fruit[J]. Plant Journal, 2018, 94(6): 1126-1140.

[22] PROVENIERS M, RUTJENS B, BRAND M, et al. The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC[J]. Plant Journal, 2007, 52(5): 899-913.

[23] COLE M, NOLTE C, WERR W. 2006. Nuclear import of the transcription factor SHOOT MERISTEMLESS depends on heterodimerization with BLH proteins expressed in discrete sub-domains of the shoot apical meristem of Arabidopsis thaliana[J]. Nucleic Acids Research, 2006, 34(4): 1281-1292.

[24] RUTJENS B, BAO D P, VAN ECK-STOUTEN E, et al. Shoot apical meristem function in Arabidopsis requires the combined activities of three BEL1-like homeodomain proteins[J]. Plant Journal, 2009, 58(4): 641-654.

[25] MAGNANI E, HAKE S. KNOX lost the OX:: The Arabidopsis KNATM gene defines a novel class of KNOX transcriptional regulators missing the homeodomain[J]. Plant Cell, 2008, 20(4): 875-887.

[26] HAMANT O, PAUTOT V. Plant development: A TALE story[J]. Comptes Rendus Biologies, 2010, 333(4): 371-381.

[27] LI E Y, BHARGAVA A, QIANG W Y, et al. The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus[J]. New Phytologist, 2012, 194(1): 102-115.

[28] ZHONG R Q, LEE C H, ZHOU J L, et al. A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis[J]. Plant Cell, 2008, 20(10): 2763-2782.

[29] BHARGAVA A, MANSFIELD S D, HALL H C, et al. MYB75 functions in regulation of secondary cell wall formation in the Arabidopsis inflorescence stem[J]. Plant Physiology, 2010, 154(3): 1428-1438.

[30] LI E Y, WANG S C, LIU Y Y, et al. Ovate family protein4 (OFP4) interaction with KNAT7 regulates secondary cell wall formation in Arabidopsis thaliana[J]. Plant Journal, 2011, 67(2): 328-341.

[31] TAO Y, CHEN M, SHU Y J, et al. Identification and functional characterization of a novel BEL1-LIKE homeobox transcription factor GmBLH4 in soybean[J]. Plant Cell Tissue and Organ Culture, 2018, 134(2): 331-344.

[32] WANG L, YANG X Y, GAO Y Q, et al. Genome-wide identification and characterization of TALE superfamily genes in soybean (Glycine max L.) [J]. International Journal of Molecular Science, 2021, 22(8): 4117.

[33] ZHAO K, ZHANG X M, CHENG Z H, et al. Comprehensive analysis of the three-amino-acid-loop-extension gene family and its tissue-differential expression in response to salt stress in poplar[J]. Plant Physiology and Biochemiatry, 2019, 136: 1-12.

[34] HAN Y X, ZHANG L L, YAN L Y, et al. Genome-wide analysis of TALE superfamily in Triticum aestivum reveals TaKNOX11-A is involved in abiotic stress response[J]. BMC Genomics, 2022, 23(1): 89.

[35] WANG Y Y, ZHAO Y J, YAN M, et al. Genome-wide identification and expression analysis of TALE gene family in pomegranate (Punica granatum L.) [J]. Agronomy-Basel, 2020, 10(6): 829.

[36] WANG J, ZHAO P, CHENG B H, et al. Identification of TALE transcription factor family and expression patterns related to fruit chloroplast development in tomato (Solanum lycopersicum L.) [J]. International Journal of Molecular Sciences, 2022, 23(9): 4507.

[37] WANG L, YANG X Y, GAO Y Q, et al. Genome-wide identification and characterization of TALE superfamily genes in soybean (Glycine max L.) [J]. International Journal of Molecular Sciences, 2021, 22(8): 4117.

[38] 赵伟, 李锡香, 王海平, 等. 萝卜 TALE 转录因子家族的鉴定与分析[J]. 生物工程学报, 2022, 38(1): 343-358.

[39] 赵长江, 宋巨奇, 都梦翔, 等. 玉米 KNOX 基因家族鉴定及组织和逆境表达分析[J]. 西北植物学报, 2021, 41(7): 1109-1119.

[40] HE Y, YANG T W, YAN S W, et al. Identification and characterization of the BEL1-like genes reveal their potential roles in plant growth and abiotic stress response in tomato[J]. International Journal of Molecular Sciences, 2022, 200: 193-205.

[41] DAI H W, ZHENG S T, ZHANG C, et al. Identification and expression analysis of the KNOX genes during organogenesis and stress responseness in Camellia sinensis (L.) O. Kuntze[J]. Molecular Genetics and Genomics, 2023, 298(6): 1559-1578.

[42] SUN R R, QIN T F, WALL S B, et al. Genome-wide identification of KNOX transcription factors in cotton and the role of GhKNOX4-A and GhKNOX22-D in response to salt and drought stress[J]. International Journal of Biological Macromolecules, 2023, 226: 1248-1260.

[43] IANNELLI M A, NICOLODI C, CORAGGIO I, et al. A novel role of Medicago truncatula KNAT3/4/5-like class 2 KNOX transcription factors in drought stress tolerance[J]. International Journal of Molecular Sciences, 2023, 24(16): 12668.

基金资助

西北农林科技大学种业创新专项(2452022116)

现代农业产业技术体系建设专项(CARS-25)

杨凌种业创新中心重点研发项目(Ylzy-sc-01)