Phân tích transcriptome toàn phần De novo của hai kiểu sinh thái Phragmites australis (cây sậy đầm lầy và cây sậy cồn) cung cấp cái nhìn mới về sự phức tạp trong transcriptome của cây sậy cồn và sự thích nghi lâu dài của nó với môi trường sa mạc

Springer Science and Business Media LLC - Tập 24 - Trang 1-23 - 2023
Jipeng Cui1,2, Tianhang Qiu1,2, Li Li1,2, Suxia Cui1,2
1College of Life Sciences, Capital Normal University, Beijing, China
2Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, China

Tóm tắt

Môi trường khắc nghiệt của sa mạc đang thay đổi một cách đáng kể từng khoảnh khắc, và phản ứng căng thẳng thích ứng nhanh chóng trong thời gian ngắn yêu cầu tiêu tốn năng lượng khổng lồ để huy động các mạng lưới điều tiết rộng rãi, điều này càng gây bất lợi cho sự sống của chính các loài thực vật sa mạc. Cây sậy cồn, đã thích nghi với môi trường sa mạc với các yếu tố sinh thái phức tạp và biến đổi, là một loại thực vật lý tưởng để nghiên cứu các cơ chế phân tử mà thực vật họ Gramineae phản ứng với sự kết hợp căng thẳng của sa mạc trong trạng thái tự nhiên của chúng. Nhưng cho đến nay, dữ liệu về nguồn gen của cây sậy vẫn còn thiếu, do đó phần lớn nghiên cứu của chúng chủ yếu tập trung vào các nghiên cứu sinh thái và sinh lý học. Trong nghiên cứu này, chúng tôi đã thu được cơ sở dữ liệu transcriptome toàn phần De novo không trùng lặp đầu tiên (FLNC) cho cây sậy đầm lầy (SR), cây sậy cồn (DR) và tổng hợp của Phragmites australis (hợp nhất dữ liệu iso-seq từ SR và DR), sử dụng công nghệ PacBio Iso-Seq và kết hợp các công cụ như Iso-Seq3 và Cogent. Chúng tôi đã xác định và mô tả các RNA không mã dài (LncRNA), yếu tố phiên mã (TF) và sự kiện cắt nối thay thế (AS) trong cây sậy dựa trên cơ sở dữ liệu transcriptome. Đồng thời, chúng tôi đã xác định và phát triển lần đầu tiên một lượng lớn các dấu hiệu trình tự biểu hiện mắc-SSR (EST-SSRs) trong cây sậy dựa trên UniTransModels. Bên cạnh đó, thông qua phân tích biểu hiện gen khác biệt của loại hoang dã và văn hóa đồng nhất, chúng tôi đã tìm thấy một số lượng lớn các yếu tố phiên mã có thể liên quan đến khả năng chịu stress sa mạc của cây sậy cồn, và tiết lộ rằng các thành viên của họ Lhc có vai trò quan trọng trong sự thích nghi lâu dài của cây sậy cồn với môi trường sa mạc. Kết quả của chúng tôi cung cấp một nguồn gen tích cực và có khả năng sử dụng cho Phragmites australis với khả năng thích nghi và kháng khuẩn rộng rãi, đồng thời cung cấp một cơ sở dữ liệu gen cho việc chú thích genome của các cây sậy sau này và các nghiên cứu về gen chức năng.

Từ khóa

#Phragmites australis #transcriptome #cây sậy đầm lầy #cây sậy cồn #RNA không mã dài #yếu tố phiên mã #sự kiện cắt nối thay thế #khả năng chịu stress sa mạc.

Tài liệu tham khảo

Guglielmi G. Climate change is turning more of Central Asia into desert. Nature. 2022. https://doi.org/10.1038/d41586-022-01667-2. Zandalinas SI, Sengupta S, Fritschi FB, Azad RK, Nechushtai R, Mittler R. The impact of multifactorial stress combination on plant growth and survival. New Phytol. 2021;230(3):1034–48. Pandey P, Irulappan V, Bagavathiannan MV, Senthil-Kumar M. Impact of Combined Abiotic and Biotic Stresses on Plant Growth and Avenues for Crop Improvement by Exploiting Physio-morphological Traits. Front Plant Sci. 2017;8:537. Eller F, Skalova H, Caplan JS, Bhattarai GP, Burger MK, Cronin JT, Guo WY, Guo X, Hazelton ELG, Kettenring KM, et al. Cosmopolitan Species As Models for Ecophysiological Responses to Global Change: The Common Reed Phragmites australis. Front Plant Sci. 1833;2017:8. Nayak SS, Pradhan S, Sahoo D, Parida A. De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance. Sci Rep. 2020;10(1):5192. Zhu XY, Chen GC, Zhang CL. Photosynthetic electron transport, photophosphorylation, and antioxidants in two ecotypes of reed (Phragmites communis Trin.) from different habitats. Photosynthetica. 2001;39:183–9. Li H, Lin WF, Shen ZJ, Peng H, Zhou JJ, Zhu XY. Physiological and proteomic analyses of different ecotypes of reed phragmites communis in adaption to natural drought and salinity. Front Plant Sci. 2021;12:720593. Lambertini C, Gustafsson MHG, Frydenberg J, Lissner J, Speranza M, Brix H. A phylogeographic study of the cosmopolitan genus Phragmites (Poaceae) based on AFLPs. Plant Syst Evol. 2006;258(3–4):161–82. Ruban AV. Evolution under the sun: optimizing light harvesting in photosynthesis. J Exp Bot. 2015;66(1):7–23. Mathur S, Agrawal D, Jajoo A. Photosynthesis: response to high temperature stress. J Photochem Photobiol B. 2014;137:116–26. Takahashi S, Murata N. How do environmental stresses accelerate photoinhibition? Trends Plant Sci. 2008;13(4):178–82. Ort DR. When there is too much light. Plant Physiol. 2001;125:29–32. Choudhury FK, Rivero RM, Blumwald E, Mittler R. Reactive oxygen species, abiotic stress and stress combination. Plant J. 2017;90(5):856–67. Mittler R. Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002;7:405–10. Qiao G, Wen XP, Zhang T. Molecular Cloning and Characterization of the Light-Harvesting Chlorophyll a/b Gene from the Pigeon pea (Cajanus cajan). Appl Biochem Biotech. 2015;177(7):1447–55. Lu Y. Identification and Roles of Photosystem II Assembly, Stability, and Repair Factors in Arabidopsis. Front Plant Sci. 2016;7:168. Morishige DT, Preiss S. Light-induced biogenesis of the light-harvesting complexes of Photosystems I and II : Gene expression and protein accumulation. Photosynth Res. 1995;44(1–2):183–90. Ouyang M, Li X, Ma J, Chi W, Xiao J, Zou M, Chen F, Lu C, Zhang L. LTD is a protein required for sorting light-harvesting chlorophyll-binding proteins to the chloroplast SRP pathway. Nat Commun. 2011;2:277. Zou Z, Yang J. Genomics analysis of the light-harvesting chlorophyll a/b-binding (Lhc) superfamily in cassava (Manihot esculenta Crantz). Gene. 2019;702:171–81. Zhao Y, Kong H, Guo Y, Zou Z. Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis. PeerJ. 2020;8: e8465. Murata N, Takahashi S, Nishiyama Y, Allakhverdiev SI. Photoinhibition of photosystem II under environmental stress. Biochim Biophys Acta. 2007;1767(6):414–21. Adams WW 3rd, Muller O, Cohu CM, Demmig-Adams B. May photoinhibition be a consequence, rather than a cause, of limited plant productivity? Photosynth Res. 2013;117(1–3):31–44. Hou L, Li G, Chen Q, Zhao J, Pan J, Lin R, Zhu X, Wang P, Wang X. De novo full length transcriptome analysis and gene expression profiling to identify genes involved in phenylethanol glycosides biosynthesis in Cistanche tubulosa. BMC Genomics. 2022;23(1):698. Xu R, Zhang J, You J, Gao L, Li Y, Zhang S, Zhu W, Shu S, Xiong C, Xiong H, et al. Full-length transcriptome sequencing and modular organization analysis of oleanolic acid- and dammarane-type saponins related gene expression patterns in Panax japonicus. Genomics. 2020;112(6):4137–47. Qiu F, Wang X, Zheng Y, Wang H, Liu X, Su X. Full-Length Transcriptome Sequencing and Different Chemotype Expression Profile Analysis of Genes Related to Monoterpenoid Biosynthesis in Cinnamomum porrectum. Int J Mol Sci. 2019;20(24):6230. Li Q, Xiang C, Xu L, Cui J, Fu S, Chen B, Yang S, Wang P, Xie Y, Wei M, et al. SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum. BMC Genomics. 2020;21(1):52. Du H, Zaman S, Hu S, Che S. Single-molecule long-read sequencing of purslane portulaca oleracea and differential gene expression related with biosynthesis of unsaturated fatty acids. Plants Basel. 2021;10(4):655. Zhang H, Liu Z, Hu A, Wu H, Zhu J, Wang F, Cao P, Yang X, Zhang H. Full-Length Transcriptome Analysis of the Halophyte Nitraria sibirica Pall. Genes (Basel). 2022;13(4):661. Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, et al. Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science. 2000;290(5499):2105–10. Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The Human Transcription Factors. Cell. 2018;172(4):650–65. Li X, Liu X, Wei J, Li Y, Tigabu M, Zhao X. Development and Transferability of EST-SSR Markers for Pinus koraiensis from Cold-Stressed Transcriptome through Illumina Sequencing. Genes (Basel). 2020;11(5):500. Sharon D, Tilgner H, Grubert F, Snyder M. A single-molecule long-read survey of the human transcriptome. Nat Biotechnol. 2013;31(11):1009. Li Y, Dai C, Hu C, Liu Z, Kang C. Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry. Plant J. 2017;90(1):164–76. Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 2012;22(6):1184–95. Zuo CM, Blow M, Sreedasyam A, Kuo RC, Ramamoorthy GK, Torres-Jerez I, Li GF, Wang M, Dilworth D, Barry K, et al. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnol Biofuels. 2018;11:170. Liu ZS, Qin JX, Tian XJ, Xu SB, Wang Y, Li HX, Wang XM, Peng HR, Yao YY, Hu ZR, et al. Global profiling of alternative splicing landscape responsive to drought, heat and their combination in wheat (Triticum aestivum L.). Plant Biotechnol J. 2018;16(3):714–26. Neilson JAD, Durnford DG. Structural and functional diversification of the light-harvesting complexes in photosynthetic eukaryotes. Photosynth Res. 2010;106(1–2):57–71. Li H, Lin WF, Shen ZJ, Peng H, Zhou JJ, Zhu XY. Physiological and Proteomic Analyses of Different Ecotypes of Reed (Phragmites communis) in Adaption to Natural Drought and Salinity. Front Plant Sci. 2021;12:720593. Tianhang Qiu SC. Evolutionary analysis for Phragmites ecotypes based on full-length plastomes. Aquat Bot. 2021;170(6): 103349. Cui SX, Hu J, Yang B, Shi L, Huang F, Tsai SN, Ngai SM, He YK, Zhang JH. Proteomic characterization of Phragmites communis in ecotypes of swamp and desert dune. Proteomics. 2009;9(16):3950–67. Li L, Chen XD, Shi L, Wang CJ, Fu B, Qiu TH, Cui SX. A Proteome Translocation Response to Complex Desert Stress Environments in Perennial Phragmites Sympatric Ecotypes with Contrasting Water Availability. Front Plant Sci. 2017;8:1–15. Zhang D, Li K, Gao J, Liu Y, Gao LZ: The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae. Front Ecol Evol 2016, 4:88. Ahmed W, Xia YS, Li RH, Bai GH, Siddique KHM, Guo PG. Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops. Genomics. 2020;112(2):1419–24. Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S, Brown JW, Crespi M. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell. 2014;30(2):166–76. Budak H, Kaya SB, Cagirici HB. Long Non-coding RNA in Plants in the Era of Reference Sequences. Front Plant Sci. 2020;11:276. Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J, Xu C, Li X, Xiao J, Zhang Q. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A. 2012;109(7):2654–9. Hou J, Lu D, Mason AS, Li B, Xiao M, An S, Fu D. Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses. Planta. 2019;250(1):23–40. Wang Y, Fan X, Lin F, He G, Terzaghi W, Zhu D, Deng XW. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc Natl Acad Sci U S A. 2014;111(28):10359–64. Yamaguchi A, Abe M. Regulation of reproductive development by non-coding RNA in Arabidopsis: to flower or not to flower. J Plant Res. 2012;125(6):693–704. Zhang YC, Chen YQ. Long noncoding RNAs: new regulators in plant development. Biochem Biophys Res Commun. 2013;436(2):111–4. Nakabayashi R, Yonekura-Sakakibara K, Urano K, Suzuki M, Yamada Y, Nishizawa T, Matsuda F, Kojima M, Sakakibara H, Shinozaki K, et al. Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. Plant J. 2014;77(3):367–79. Gao J, Wang M-J, Wang J-J, Lu H-P, Liu J-X: bZIP17 regulates heat stress tolerance at reproductive stage in Arabidopsis. aBIOTECH 2021. Shao HB, Wang HY, Tang XL. NAC transcription factors in plant multiple abiotic stress responses: progress and prospects. Front Plant Sci. 2015;6:902. Nakashima K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K. NAC transcription factors in plant abiotic stress responses. Bba-Gene Regul Mech. 2012;1819(2):97–103. Wang CT, Ru JN, Liu YW, Yang JF, Li M, Xu ZS, Fu JD: The Maize WRKY Transcription Factor ZmWRKY40 Confers Drought Resistance in Transgenic Arabidopsis. International Journal of Molecular Sciences 2018, 19(9). Liu R, Xu YH, Jiang SC, Lu K, Lu YF, Feng XJ, Wu Z, Liang S, Yu YT, Wang XF, et al. Light-harvesting chlorophyll a/b-binding proteins, positively involved in abscisic acid signalling, require a transcription repressor, WRKY40, to balance their function. J Exp Bot. 2013;64(18):5443–56. Feng K, Hou XL, Xing GM, Liu JX, Duan AQ, Xu ZS, Li MY, Zhuang J, Xiong AS. Advances in AP2/ERF super-family transcription factors in plant. Crit Rev Biotechnol. 2020;40(6):750–76. Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W. Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet. 2002;104(2–3):399–407. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S: Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res 2001, 11(8):1441–1452. Xiong YL, Liu WH, Xiong Y, Yu QQ, Ma X, Lei X, Zhang XQ, Li DX: Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers. Peerj. 2019;7:e8038. Sun M, Zhao Y, Shao X, Ge J, Tang X, Zhu P, Wang J, Zhao T. EST-SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb). Appl Bionics Biomech. 2022;2022:7641048. Liang XQ, Chen XP, Hong YB, Liu HY, Zhou GY, Li SX, Guo BZ: Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. Bmc Plant Biology 2009;9:35. Wang L, Zhang R, Geng M, Qin Y, Liu H, Li L, Li M: De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae). 3 Biotech 2021;11(9):420. Zhang ZY, Xie WG, Zhao YQ, Zhang JC, Wang N, Ntakirutimana F, Yan JJ, Wang YR: EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species. BMC Plant Biol 2019; 19:235. Sun M, Dong ZX, Yang J, Wu WD, Zhang CL, Zhang JB, Zhao JM, Xiong Y, Jia SG, Ma X. Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers. BMC Plant Biol. 2021;21(1):264. Liu LY, Fan XF, Tan PH, Wu JY, Zhang H, Han C, Chen C, Xun LL, Guo WE, Chang ZH et al: The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species. Bmc Plant Biology 2021, 21(1). Chagne D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera MT, Vendramin GG, Garcia V, Frigerio JM, Echt C, et al. Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet. 2004;109(6):1204–14. Wang ET, Sandberg R, Luo SJ, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456(7221):470–6. Filichkin S, Priest HD, Megraw M, Mockler TC. Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress. Curr Opin Plant Biol. 2015;24:125–35. Laloum T, Martin G, Duque P. Alternative Splicing Control of Abiotic Stress Responses. Trends Plant Sci. 2018;23(2):140–50. Petrillo E, Herz MAG, Fuchs A, Reifer D, Fuller J, Yanovsky MJ, Simpson C, Brown JWS, Barta A, Kalyna M, et al. A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing. Science. 2014;344(6182):427–30. Herz MAG, Kubaczka MG, Brzyzek G, Servi L, Krzyszton M, Simpson C, Brown J, Swiezewski S, Petrillo E, Kornblihtt AR. Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation. Mol Cell. 2019;73(5):1066. Dong CL, He F, Berkowitz O, Liu JX, Cao PF, Tang M, Shi HC, Wang WJ, Li QL, Shen ZG, et al. Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa). Plant Cell. 2018;30(10):2267–85. John S, Olas JJ, Mueller-Roeber B. Regulation of alternative splicing in response to temperature variation in plants. J Exp Bot. 2021;72(18):6150–63. Filichkin SA, Mockler TC. Unproductive alternative splicing and nonsense mRNAs: a widespread phenomenon among plant circadian clock genes. Biol Direct. 2012;7:20 Published 2012 Jul 2. Niklas KJ, Dunker AK, Yruela I. The evolutionary origins of cell type diversification and the role of intrinsically disordered proteins. J Exp Bot. 2018;69(7):1437–46. Buljan M, Chalancon G, Dunker AK, et al. Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr Opin Struct Biol. 2013;23(3):443–50. Göhring J, Jacak J, Barta A. Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis. Plant Cell. 2014;26(2):754–64. Hartmann L, Wießner T, Wachter A. Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression. Plant Physiol. 2018;176(4):2886–903. Reddy ASN, Marquez Y, Kalyna M, Barta A. Complexity of the Alternative Splicing Landscape in Plants. Plant Cell. 2013;25(10):3657–83. Chaudhary S, Jabre I, Reddy ASN, Staiger D, Syed NH. Perspective on Alternative Splicing and Proteome Complexity in Plants. Trends Plant Sci. 2019;24(6):496–506. Li Y, Guo Q, Liu P, Huang J, Zhang S, Yang G, Wu C, Zheng C, Yan K. Dual roles of the serine/arginine-rich splicing factor SR45a in promoting and interacting with nuclear cap-binding complex to modulate the salt-stress response in Arabidopsis. New Phytol. 2021;230(2):641–55. Niklas KJ, Bondos SE, Dunker AK, Newman SA. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications. Front Cell Dev Biol. 2015;3:8 Published 2015 Feb 26. Smithers B, Oates ME, Gough J. Splice junctions are constrained by protein disorder. Nucleic Acids Res. 2015;43(10):4814–22. Paul MJ, Foyer CH. Sink regulation of photosynthesis. J Exp Bot. 2001;52(360):1383–400. Chaves MM, Flexas J, Pinheiro C. Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot-London. 2009;103(4):551–60. Perlikowski D, Lechowicz K, Pawlowicz I, Arasimowicz-Jelonek M, Kosmala A. Scavenging of nitric oxide up-regulates photosynthesis under drought in Festuca arundinacea and F. glaucescens but reduces their drought tolerance. Sci Rep. 2022;12(1):650. Dong HP, Dong YL, Cui L, Balamurugan S, Gao J, Lu SH, Jiang T. High light stress triggers distinct proteomic responses in the marine diatom Thalassiosira pseudonana. BMC Genomics. 2016;17(1):994. Niyogi: <Photoprotection revisited Genetic and molecular approaches.pdf>. 1999. Pinnola A. The rise and fall of Light-Harvesting Complex Stress-Related proteins as photoprotection agents during evolution. J Exp Bot. 2019;70(20):5527–35. Rochaix JD, Bassi R. LHC-like proteins involved in stress responses and biogenesis/repair of the photosynthetic apparatus. Biochem J. 2019;476:581–93. Zou Z, Li MY, Jia RZ, Zhao H, He PP, Zhang YL, Guo AP: Genes encoding light-harvesting chlorophyll a/b-binding proteins in papaya (Carica papaya L.) and insight into lineage-specific evolution in Brassicaceae. Gene 2020,748:144685. Liu XQ, Liu RL, Li Y, Shen X, Zhong SW, Shi H. EIN3 and PIF3 Form an Interdependent Module That Represses Chloroplast Development in Buried Seedlings. Plant Cell. 2017;29(12):3051–67. Xu YH, Liu R, Yan L, Liu ZQ, Jiang SC, Shen YY, Wang XF, Zhang DP. Light-harvesting chlorophyll a/b-binding proteins are required for stomatal response to abscisic acid in Arabidopsis. J Exp Bot. 2012;63(3):1095–106. Cazzaniga S, Kim M, Bellamoli F, Jeong J, Lee S, Perozeni F, Pompa A, Jin E, Ballottari M. Photosystem II antenna complexes CP26 and CP29 are essential for nonphotochemical quenching in Chlamydomonas reinhardtii. Plant Cell Environ. 2020;43(2):496–509. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–100. Alamancos GP, Pages A, Trincado JL, Bellora N, Eyras E. Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA. 2015;21(9):1521–31. Chen YX, Chen YS, Shi CM, Huang ZB, Zhang Y, Li SK, Li Y, Ye J, Yu C, Li Z et al: SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 2017, 7(1). Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. Kim D, Landmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357-U121. Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. 2019;47(8);e47. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. Yu GC, Wang LG, Han YY, He QY. clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters. OMICS. 2012;16(5):284–7. Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18(4):366–8. Buchfink BXC, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60. Altschul S, Madden T, Schaffer A, Zhang JH, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Faseb J. 1998;12(8):A1326–A1326. Kanehisa, M. and Goto, S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000 Jan 1;28(1):27–30. Kanehisa M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 2019;28(11):1947–51. Cantalapiedra CP, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol. 2021;38(12):5825–9. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol. 2001;305(3):567–80. E. L.L. Sonnhammer, G. von Heijne, and A. Krogh. A hidden Markov model for predicting transmembrane helices in protein sequences. In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175–182, Menlo Park, 1998. AAAI Press. Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020;13(8):1194–202.