Comprehensive identification of GASA genes in sunflower and expression profiling in response to drought.
GASA
Drought
Evolution
Expression analysis
Sunflower
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
14 Oct 2024
14 Oct 2024
Historique:
received:
06
07
2024
accepted:
03
10
2024
medline:
15
10
2024
pubmed:
15
10
2024
entrez:
14
10
2024
Statut:
epublish
Résumé
Drought stress poses a critical threat to global crop yields and sustainable agriculture. The GASA genes are recognized for their pivotal role in stress tolerance and plant growth, but little is known about how they function in sunflowers. The investigation aimed to identify and elucidate the role of HaGASA genes in conferring sunflowers with drought tolerance. Twenty-seven different HaGASA gene family members were found in this study that were inconsistently located across eleven sunflower chromosomes. Phylogeny analysis revealed that the sunflower HaGASA genes were divided into five subgroups by comparing GASA genes with those from Arabidopsis, peanut, and soybean, with members within each subgroup displaying similar conserved motifs and gene structures. In-silico evaluation of cis-regulatory elements indicated the existence of specific elements associated with stress-responsiveness being the most abundant, followed by hormone, light, and growth-responsive elements. Transcriptomic data from the NCBI database was utilized to assess the HaGASA genes expression profile in different sunflower varieties under drought conditions. The HaGASA genes expression across ten sunflower genotypes under drought stress, revealed 14 differentially expressed HaGASA genes, implying their active role in the plant's stress response. The expression in different organs revealed that HaGASA2, HaGASA11, HaGASA17, HaGASA19, HaGASA21 and HaGASA26 displayed maximum expression in the stem. Our findings implicate HaGASA genes in mediating sunflower growth maintenance and adaptation to abiotic stress, particularly drought. The findings, taken together, provided a basic understanding of the structure and potential functions of HaGASA genes, setting the framework for further functional investigations into their roles in drought stress mitigation and crop improvement strategies.
Identifiants
pubmed: 39402437
doi: 10.1186/s12864-024-10860-8
pii: 10.1186/s12864-024-10860-8
doi:
Substances chimiques
Plant Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
954Subventions
Organisme : Princess Nourah Bint Abdulrahman University
ID : PNURSP2024R459
Organisme : Princess Nourah Bint Abdulrahman University
ID : PNURSP2024R459
Informations de copyright
© 2024. The Author(s).
Références
Campos ML, et al. The role of antimicrobial peptides in plant immunity. J Exp Bot. 2018;69(21):4997–5011.
pubmed: 30099553
doi: 10.1093/jxb/ery294
Sadelaji S, et al. Ib-AMP4 antimicrobial peptide as a treatment for skin and systematic infection of methicillin-resistant Staphylococcus aureus (MRSA). Iran J Basic Med Sci. 2022;25(2):232.
pubmed: 35655604
pmcid: 9124539
Liu L, et al. Small but powerful: RALF peptides in plant adaptive and developmental responses. Plant Sci. 2024;343:112085. https://doi.org/10.1016/j.plantsci.2024.112085 .
Jangra R, et al. Duplicated antagonistic EPF peptides optimize grass stomatal initiation. Development. 2021;148(16):dev199780.
pubmed: 34328169
doi: 10.1242/dev.199780
Caine RS, et al. An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens. Development. 2016;143(18):3306–14.
pubmed: 27407102
pmcid: 5047656
Mizuta Y, Higashiyama T. Chemical signaling for pollen tube guidance at a glance. J Cell Sci. 2018;131(2):jcs208447.
pubmed: 29378835
doi: 10.1242/jcs.208447
Shahin-Kaleybar B, et al. Isolation of cysteine-rich peptides from Citrullus colocynthis. Biomolecules. 2020;10(9):1326.
pubmed: 32948080
pmcid: 7565491
doi: 10.3390/biom10091326
Silverstein KA, et al. Small cysteine-rich peptides resembling antimicrobial peptides have been under‐predicted in plants. Plant J. 2007;51(2):262–80.
pubmed: 17565583
doi: 10.1111/j.1365-313X.2007.03136.x
Ahmad B, et al. Genome-wide characterization and expression profiling of GASA genes during different stages of seed development in grapevine (Vitis vinifera L.) predict their involvement in seed development. Int J Mol Sci. 2020;21(3):1088.
pubmed: 32041336
pmcid: 7036793
doi: 10.3390/ijms21031088
Shi L, Olszewski NE. Gibberellin and abscisic acid regulate GAST1 expression at the level of transcription. Plant Mol Biol. 1998;38:1053–60.
pubmed: 9869411
doi: 10.1023/A:1006007315718
Shaban M, et al. Genome-wide dissection, characterization, and expression profiling of cotton GASA genes reveal their importance in regulating abiotic stresses. 2021.
Zhang S, Wang X. Expression pattern of GASA, downstream genes of DELLA, in Arabidopsis. Chin Sci Bull. 2008;53(24):3839–46.
doi: 10.1007/s11434-008-0525-9
Ben-Nissan G, et al. GIP, a Petunia hybrida GA‐induced cysteine‐rich protein: a possible role in shoot elongation and transition to flowering. Plant J. 2004;37(2):229–38.
pubmed: 14690507
doi: 10.1046/j.1365-313X.2003.01950.x
Aubert D, et al. Expression patterns of GASA genes in Arabidopsis thaliana: the GASA4 gene is up-regulated by gibberellins in meristematic regions. Plant Mol Biol. 1998;36:871–83.
pubmed: 9520278
doi: 10.1023/A:1005938624418
Porto WF, Franco OL. Theoretical structural insights into the snakin/GASA family. Peptides. 2013;44:163–7.
pubmed: 23578978
doi: 10.1016/j.peptides.2013.03.014
Furukawa T, Sakaguchi N, Shimada H. Two OsGASR genes, rice GAST homologue genes that are abundant in proliferating tissues, show different expression patterns in developing panicles. Genes Genet Syst. 2006;81(3):171–80.
pubmed: 16905871
doi: 10.1266/ggs.81.171
Fan S, et al. Comprehensive analysis of GASA family members in the Malus domestica genome: identification, characterization, and their expressions in response to apple flower induction. BMC Genomics. 2017;18:1–19.
doi: 10.1186/s12864-017-4213-5
Zhang K, et al. Genome-wide identification of GASA gene family in ten cucurbitaceae species and expression analysis in cucumber. Agronomy. 2022;12(8):1978.
doi: 10.3390/agronomy12081978
Qiao K, et al. Identification, characterization, and expression profiles of the GASA genes in cotton. J Cotton Res. 2021;4:1–16.
doi: 10.1186/s42397-021-00081-9
Wu Y, et al. Comprehensive analysis of GASA family members in the peanut genome: identification, characterization, and their expressions in response to pod development. Agronomy. 2022;12(12):3067.
doi: 10.3390/agronomy12123067
Cheng X, et al. Identification and analysis of the GASR gene family in common wheat (Triticum aestivum L.) and characterization of TaGASR34, a gene associated with seed dormancy and germination. Front Genet. 2019;10:980.
pubmed: 31681420
pmcid: 6813915
doi: 10.3389/fgene.2019.00980
Ahmad MZ, et al. A genome-wide approach to the comprehensive analysis of GASA gene family in Glycine max. Plant Mol Biol. 2019;100:607–20.
pubmed: 31123969
doi: 10.1007/s11103-019-00883-1
Filiz E, Kurt F. Antimicrobial peptides Snakin/GASA gene family in sorghum (Sorghum bicolor): genome-wide identification and bioinformatics analyses. Gene Rep. 2020;20:100766.
doi: 10.1016/j.genrep.2020.100766
Sun B, et al. Genome-wide identification and expression analysis of the GASA gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genomics. 2023;24(1):668.
pubmed: 37932701
pmcid: 10629197
doi: 10.1186/s12864-023-09773-9
Nahirñak V, et al. Genome-wide analysis of the Snakin/GASA gene family in Solanum Tuberosum Cv. Kennebec. Am J Potato Res. 2016;93:172–88.
doi: 10.1007/s12230-016-9494-8
Wu T, et al. Analysis of CcGASA family members in Citrus Clementina (Hort. Ex Tan.) By a genome-wide approach. BMC Plant Biol. 2021;21:1–18.
doi: 10.1186/s12870-021-03326-6
Yang M, et al. Genome-wide identification and characterization of Gibberellic Acid-stimulated Arabidopsis Gene Family in Pineapple (Ananas comosus). Int J Mol Sci. 2023;24(23):17063.
pubmed: 38069384
pmcid: 10706908
doi: 10.3390/ijms242317063
Li Z, et al. Genome-wide identification and characterization of GASA gene family in Nicotiana tabacum. Front Genet. 2022;12:768942.
pubmed: 35178069
pmcid: 8844377
doi: 10.3389/fgene.2021.768942
Han S, et al. Genome-wide comprehensive analysis of the GASA gene family in Populus. Int J Mol Sci. 2021;22(22):12336.
pubmed: 34830215
pmcid: 8624709
doi: 10.3390/ijms222212336
Büyük I, et al. Identification and characterization of the Pvul-GASA gene family in thePhaseolus Vulgaris and expression patterns under salt stress. Turkish J Bot. 2021;45(7):655–70.
doi: 10.3906/bot-2101-13
Su D, et al. Genome-wide characterization of the tomato GASA family identifies SlGASA1 as a repressor of fruit ripening. Hortic Res. 2023;10(1):uhac222.
pubmed: 36643743
doi: 10.1093/hr/uhac222
Zimmermann R, Sakai H, Hochholdinger F. The gibberellic acid stimulated-like gene family in maize and its role in lateral root development. Plant Physiol. 2010;152(1):356–65.
pubmed: 19926801
pmcid: 2799369
doi: 10.1104/pp.109.149054
de la Fuente JI, et al. The strawberry gene FaGAST affects plant growth through inhibition of cell elongation. J Exp Bot. 2006;57(10):2401–11.
pubmed: 16804055
doi: 10.1093/jxb/erj213
Wang L, et al. OsGSR1 is involved in crosstalk between gibberellins and brassinosteroids in rice. Plant J. 2009;57(3):498–510.
pubmed: 18980660
doi: 10.1111/j.1365-313X.2008.03707.x
Alonso-Ramírez A, et al. Evidence for a role of gibberellins in salicylic acid-modulated early plant responses to abiotic stress in Arabidopsis seeds. Plant Physiol. 2009;150(3):1335–44.
pubmed: 19439570
pmcid: 2705047
doi: 10.1104/pp.109.139352
Li K-L, et al. GsGASA1 mediated root growth inhibition in response to chronic cold stress is marked by the accumulation of DELLAs. J Plant Physiol. 2011;168(18):2153–60.
pubmed: 21855169
doi: 10.1016/j.jplph.2011.07.006
Li X, et al. OsGASR9 positively regulates grain size and yield in rice (Oryza sativa). Plant Sci. 2019;286:17–27.
pubmed: 31300138
doi: 10.1016/j.plantsci.2019.03.008
Wang H, et al. Transcriptome analyses from mutant Salvia miltiorrhiza reveals important roles for SmGASA4 during plant development. Int J Mol Sci. 2018;19(7):2088.
pubmed: 30021961
pmcid: 6073587
doi: 10.3390/ijms19072088
Segura A, et al. Snakin-1, a peptide from potato that is active against plant pathogens. Mol Plant Microbe Interact. 1999;12(1):16–23.
pubmed: 9885189
doi: 10.1094/MPMI.1999.12.1.16
Mao Z, et al. The new CaSn gene belonging to the snakin family induces resistance against root-knot nematode infection in pepper. Phytoparasitica. 2011;39:151–64.
doi: 10.1007/s12600-011-0149-5
Khan S, et al. Sunflower oil: efficient oil source for human consumption. Emergent life Sci Res. 2015;1:1–3.
Fulda S, et al. Physiology and proteomics of drought stress acclimation in sunflower (Helianthus annuus L). Plant Biol. 2011;13(4):632–42.
pubmed: 21668604
doi: 10.1111/j.1438-8677.2010.00426.x
Chen L, Yang J-y, Wang D. Phytoremediation of uranium and cadmium contaminated soils by sunflower (Helianthus annuus L.) enhanced with biodegradable chelating agents. J Clean Prod. 2020;263:121491.
doi: 10.1016/j.jclepro.2020.121491
Bashir SS, et al. Plant drought stress tolerance: understanding its physiological, biochemical and molecular mechanisms. Biotechnol Biotechnol Equip. 2021;35(1):1912–25.
doi: 10.1080/13102818.2021.2020161
Zhang C, et al. Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress. PeerJ. 2024;12:e17808.
pubmed: 39099650
pmcid: 11296301
doi: 10.7717/peerj.17808
Li W, et al. Genome-wide identification and comprehensive analysis of the NAC transcription factor family in sunflower during salt and drought stress. Sci Rep. 2021;11(1):19865.
pubmed: 34615898
pmcid: 8494813
doi: 10.1038/s41598-021-98107-4
Song H, et al. Genome-wide identification and expression analysis of the Dof gene family reveals their involvement in hormone response and abiotic stresses in sunflower (Helianthus annuus L). Gene. 2024;910:148336.
pubmed: 38447680
doi: 10.1016/j.gene.2024.148336
Li J, et al. Genome-wide identification of MYB genes and expression analysis under different biotic and abiotic stresses in Helianthus annuus L. Ind Crops Prod. 2020;143:111924.
doi: 10.1016/j.indcrop.2019.111924
Hussain M, et al. Genome-wide analysis of plant specific YABBY transcription factor gene family in carrot (Dacus carota) and its comparison with Arabidopsis. BMC Genomic Data. 2024;25(1):26.
pubmed: 38443818
pmcid: 10916311
doi: 10.1186/s12863-024-01210-4
Khatun K, et al. Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses. BMC Genomics. 2021;22:1–17.
doi: 10.1186/s12864-021-08019-w
Maqsood H, et al. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. Front Plant Sci. 2022;13:1031679.
pubmed: 36507398
pmcid: 9731513
doi: 10.3389/fpls.2022.1031679
Horton P, et al. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007;35(suppl2):W585-7.
pubmed: 17517783
pmcid: 1933216
doi: 10.1093/nar/gkm259
Zhao L, et al. Genome-wide identification and analysis of the evolution and expression pattern of the HVA22 gene family in three wild species of tomatoes. PeerJ. 2023;11:e14844.
pubmed: 36815985
pmcid: 9933743
doi: 10.7717/peerj.14844
Ma Q, et al. Genomic analysis reveals phylogeny of Zygophyllales and mechanism for water retention of a succulent xerophyte. Plant Physiol. 2024;195.
Letunic I, Bork P. Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 2024;52.
Hu B, et al. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2015;31(8):1296–7.
pubmed: 25504850
doi: 10.1093/bioinformatics/btu817
Dai Y, et al. Evolution and expression of the meprin and TRAF homology domain-containing Gene Family in Solanaceae. Int J Mol Sci. 2023;24(10):8782.
pubmed: 37240124
pmcid: 10218331
doi: 10.3390/ijms24108782
Li X, et al. Genome-wide identification of NAC transcription factor family in Juglans mandshurica and their expression analysis during the fruit development and ripening. Int J Mol Sci. 2021;22(22):12414.
pubmed: 34830294
pmcid: 8625062
doi: 10.3390/ijms222212414
Akter N, et al. Genome-wide identification and characterization of protein phosphatase 2 C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses. PLoS ONE. 2024;19(3):e0298543.
pubmed: 38507444
pmcid: 10954154
doi: 10.1371/journal.pone.0298543
Lei Y, et al. Characterization and gene expression patterns analysis implies BSK family genes respond to salinity stress in cotton. Front Genet. 2023;14:1169104.
pubmed: 37351349
pmcid: 10282553
doi: 10.3389/fgene.2023.1169104
Song H, et al. Genome-wide characterization and comprehensive analysis of NAC transcription factor family in Nelumbo nucifera. Front Genet. 2022;13:901838.
pubmed: 35754820
pmcid: 9214227
doi: 10.3389/fgene.2022.901838
Wang Y et al. Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX. Nat Protoc. 2024:1–24.
Berendzen KW, et al. Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. BMC Bioinformatics. 2006;7:1–19.
doi: 10.1186/1471-2105-7-522
Ho C-L, Geisler M. Genome-wide computational identification of biologically significant cis-regulatory elements and associated transcription factors from rice. Plants. 2019;8(11):441.
pubmed: 31652796
pmcid: 6918188
doi: 10.3390/plants8110441
Luo X, et al. The evolution of the WUSCHEL-related homeobox gene family in dendrobium species and its role in sex organ development in D. chrysotoxum. Int J Mol Sci. 2024;25(10):5352.
pubmed: 38791390
pmcid: 11121392
doi: 10.3390/ijms25105352
Patel M, et al. Antioxidant effects and potential molecular mechanism of action of Diplocyclos Palmatus (L.) C. Jeffrey Fruits based on systematic network pharmacology with experimental validation. J Mol Struct. 2024;1313:138638.
doi: 10.1016/j.molstruc.2024.138638
Bu D, et al. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res. 2021;49(W1):W317-25.
pubmed: 34086934
pmcid: 8265193
doi: 10.1093/nar/gkab447
Guo Z, et al. PmiREN: a comprehensive encyclopedia of plant miRNAs. Nucleic Acids Res. 2020;48(D1):D1114-21.
pubmed: 31602478
doi: 10.1093/nar/gkz894
Tabassum N, et al. Genome-wide in-silico analysis of ethylene biosynthesis gene family in Musa acuminata L. and their response under nutrient stress. Sci Rep. 2024;14(1):558.
pubmed: 38177217
pmcid: 10767074
doi: 10.1038/s41598-023-51075-3
Gody L, et al. Transcriptomic data of leaves from eight sunflower lines and their sixteen hybrids under water deficit. OCL. 2020;27:48.
doi: 10.1051/ocl/2020044
Wu Y, et al. Genome-wide analysis of TCP transcription factor family in sunflower and identification of HaTCP1 involved in the regulation of shoot branching. BMC Plant Biol. 2023;23(1):222.
pubmed: 37101166
pmcid: 10134548
doi: 10.1186/s12870-023-04211-0
Yan J, et al. Genome-wide association study and genetic mapping of BhWAX conferring mature fruit cuticular wax in wax gourd. BMC Plant Biol. 2022;22(1):539.
pubmed: 36401157
pmcid: 9675113
doi: 10.1186/s12870-022-03931-z
Sánchez D, et al. Exon-intron structure and evolution of the lipocalin gene family. Mol Biol Evol. 2003;20(5):775–83.
pubmed: 12679526
doi: 10.1093/molbev/msg079
Cheng L, et al. Genome-wide identification, classification, and expression analysis of amino acid transporter gene family in Glycine max. Front Plant Sci. 2016;7:515.
pubmed: 27148336
pmcid: 4837150
doi: 10.3389/fpls.2016.00515
Pond SLK, Poon AF, Frost SD. Estimating selection pressures on alignments of coding sequences. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge, UK: Cambridge University Press; 2009. p. 419–90.
doi: 10.1017/CBO9780511819049.016
Newton IL, et al. Comparative genomics of two closely related Wolbachia with different reproductive effects on hosts. Genome Biol Evol. 2016;8(5):1526–42.
pubmed: 27189996
pmcid: 4898810
doi: 10.1093/gbe/evw096
Spitz F, Furlong EE. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13(9):613–26.
pubmed: 22868264
doi: 10.1038/nrg3207
Srinivasan C, et al. Addiction-associated genetic variants implicate brain cell type-and region-specific cis-regulatory elements in addiction neurobiology. J Neurosci. 2021;41(43):9008–30.
pubmed: 34462306
pmcid: 8549541
doi: 10.1523/JNEUROSCI.2534-20.2021
Huan T, et al. Genome-wide identification of microRNA expression quantitative trait loci. Nat Commun. 2015;6(1):6601.
pubmed: 25791433
doi: 10.1038/ncomms7601
Chen X, et al. MicroRNAs and complex diseases: from experimental results to computational models. Brief Bioinform. 2019;20(2):515–39.
pubmed: 29045685
doi: 10.1093/bib/bbx130
Vos M, et al. The asymmetric response concept explains ecological consequences of multiple stressor exposure and release. Sci Total Environ. 2023;872:162196.
pubmed: 36781140
doi: 10.1016/j.scitotenv.2023.162196
Mittler R. Abiotic stress, the field environment and stress combination. Trends Plant Sci. 2006;11(1):15–9.
pubmed: 16359910
doi: 10.1016/j.tplants.2005.11.002
Huang J, et al. Evaluation of regional estimates of winter wheat yield by assimilating three remotely sensed reflectance datasets into the coupled WOFOST–PROSAIL model. Eur J Agron. 2019;102:1–13.
doi: 10.1016/j.eja.2018.10.008
Prasch CM, Sonnewald U. Simultaneous application of heat, drought, and virus to Arabidopsis plants reveals significant shifts in signaling networks. Plant Physiol. 2013;162(4):1849–66.
pubmed: 23753177
pmcid: 3729766
doi: 10.1104/pp.113.221044
Zhou J, et al. H2O2 mediates the crosstalk of brassinosteroid and abscisic acid in tomato responses to heat and oxidative stresses. J Exp Bot. 2014;65(15):4371–83.
pubmed: 24899077
pmcid: 4112640
doi: 10.1093/jxb/eru217
Song Y, Miao Y, Song CP. Behind the scenes: the roles of reactive oxygen species in guard cells. New Phytologist. 2014;201(4):1121–40. https://doi.org/10.1111/nph.12565 .
doi: 10.1111/nph.12565
pubmed: 24188383
Zhou Rong ZR, et al. High throughput sequencing of circRNAs in tomato leaves responding to multiple stresses of drought and heat. 2020.
Mu Y, et al. Cucumber CsBPCs regulate the expression of CsABI3 during seed germination. Front Plant Sci. 2017;8:459.
pubmed: 28421094
pmcid: 5376566
doi: 10.3389/fpls.2017.00459
Yin L, et al. Wavelet analysis of dam injection and discharge in three gorges dam and reservoir with precipitation and river discharge. Water. 2022;14(4):567.
doi: 10.3390/w14040567
Su T, et al. Molecular and biological properties of snakins: the foremost cysteine-rich plant host defense peptides. J Fungi. 2020;6(4):220.
doi: 10.3390/jof6040220
Sami A, et al. Genome-wide identification and in-silico expression analysis of CCO gene family in sunflower (Helianthus Annnus) against abiotic stress. Plant Mol Biol. 2024;114(2):34.
pubmed: 38568355
pmcid: 10991017
doi: 10.1007/s11103-024-01433-0
Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982;157(1):105–32.
pubmed: 7108955
doi: 10.1016/0022-2836(82)90515-0
Gamage DG, et al. Applicability of instability index for in vitro protein stability prediction. Protein Pept Lett. 2019;26(5):339–47.
pubmed: 30816075
doi: 10.2174/0929866526666190228144219
Itzhak DN, et al. Global, quantitative and dynamic mapping of protein subcellular localization. Elife. 2016;5:e16950.
pubmed: 27278775
pmcid: 4959882
doi: 10.7554/eLife.16950
Zhang S, et al. GASA5, a regulator of flowering time and stem growth in Arabidopsis thaliana. Plant Mol Biol. 2009;69:745–59.
pubmed: 19190987
doi: 10.1007/s11103-009-9452-7
Meyer RS, Purugganan MD. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet. 2013;14(12):840–52.
pubmed: 24240513
doi: 10.1038/nrg3605
Gadagkar SR, Rosenberg MS, Kumar S. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Experimental Zool Part B Mol Dev Evol. 2005;304(1):64–74.
doi: 10.1002/jez.b.21026
Richardson R, et al. Meta-research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results. Elife. 2024;12:RP93429.
pubmed: 38546716
pmcid: 10977968
doi: 10.7554/eLife.93429
Barker D, Pagel M. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol. 2005;1(1):e3.
pubmed: 16103904
pmcid: 1183509
doi: 10.1371/journal.pcbi.0010003
Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein‐coding DNA and eukaryotic complexity. BioEssays. 2007;29(3):288–99.
pubmed: 17295292
doi: 10.1002/bies.20544
Beer MA, Tavazoie S. Predicting gene expression from sequence. Cell. 2004;117(2):185–98.
pubmed: 15084257
doi: 10.1016/S0092-8674(04)00304-6
Wray GA, et al. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 2003;20(9):1377–419.
pubmed: 12777501
doi: 10.1093/molbev/msg140
Mayer KF, et al. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell. 2011;23(4):1249–63.
pubmed: 21467582
pmcid: 3101540
doi: 10.1105/tpc.110.082537
Excoffier L, Foll M, Petit RJ. Genetic consequences of range expansions. Annu Rev Ecol Evol Syst. 2009;40:481–501.
doi: 10.1146/annurev.ecolsys.39.110707.173414
Yang X, et al. OsTTG1, a WD40 repeat gene, regulates anthocyanin biosynthesis in rice. Plant J. 2021;107(1):198–214.
pubmed: 33884679
doi: 10.1111/tpj.15285
Liu J, et al. Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective. Genome Biol. 2008;9:1–17.
doi: 10.1186/gb-2008-9-4-r69
Hurst LD. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002;18(9):486–7.
pubmed: 12175810
doi: 10.1016/S0168-9525(02)02722-1
Massingham T, Goldman N. Detecting amino acid sites under positive selection and purifying selection. Genetics. 2005;169(3):1753–62.
pubmed: 15654091
pmcid: 1449526
doi: 10.1534/genetics.104.032144
Ayoubi TA, Van De Yen WJ. Regulation of gene expression by alternative promoters. FASEB J. 1996;10(4):453–60.
pubmed: 8647344
doi: 10.1096/fasebj.10.4.8647344
Cheng P, et al. Inclusion of root water absorption and reinforcement in upper bound limit stability analysis of vegetated slopes. Comput Geotech. 2024;169:106227.
doi: 10.1016/j.compgeo.2024.106227
Liu J-H, Peng T, Dai W. Critical cis-acting elements and interacting transcription factors: key players associated with abiotic stress responses in plants. Plant Mol Biology Report. 2014;32:303–17.
doi: 10.1007/s11105-013-0667-z
Yi J, et al. Assessing soil water balance to optimize irrigation schedules of flood-irrigated maize fields with different cultivation histories in the arid region. Agric Water Manage. 2022;265:107543.
doi: 10.1016/j.agwat.2022.107543
Khraiwesh B, et al. Transcriptional control of gene expression by microRNAs. Cell. 2010;140(1):111–22.
pubmed: 20085706
doi: 10.1016/j.cell.2009.12.023
Krützfeldt J, Poy MN, Stoffel M. Strategies to determine the biological function of microRNAs. Nat Genet. 2006;38(Suppl 6):S14-9.
pubmed: 16736018
doi: 10.1038/ng1799
Hausser J, Zavolan M. Identification and consequences of miRNA–target interactions—beyond repression of gene expression. Nat Rev Genet. 2014;15(9):599–612.
pubmed: 25022902
doi: 10.1038/nrg3765
Yin L, et al. U-Net-LSTM: time series-enhanced lake boundary prediction model. Land. 2023;12(10):1859.
doi: 10.3390/land12101859
Zhao Y, et al. Characterizing uncertainty in process-based hydraulic modeling, exemplified in a semiarid Inner Mongolia steppe. Geoderma. 2023;440:116713.
doi: 10.1016/j.geoderma.2023.116713
Seleiman MF, et al. Drought stress impacts on plants and different approaches to alleviate its adverse effects. Plants. 2021;10(2):259.
pubmed: 33525688
pmcid: 7911879
doi: 10.3390/plants10020259
Muhammad Asad U, Zia MAB. Morphological characterization of diverse wheat genotypes for yield and related traits under drought condition. Int J Nat Eng Sci. 2023;17(3):87–94.
Pan X, et al. Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses. PeerJ. 2023;11:e15310.
pubmed: 37163152
pmcid: 10164373
doi: 10.7717/peerj.15310
Julca I, Tan QW, Mutwil M. Toward kingdom-wide analyses of gene expression. Trends Plant Sci. 2023;28(2):235–49.
pubmed: 36344371
doi: 10.1016/j.tplants.2022.09.007
Yin L, et al. Spatial and wavelet analysis of precipitation and river discharge during operation of the Three Gorges Dam, China. Ecol Ind. 2023;154:110837.
doi: 10.1016/j.ecolind.2023.110837
Nahirñak V, et al. Potato snakin-1 gene silencing affects cell division, primary metabolism, and cell wall composition. Plant Physiol. 2012;158(1):252–63.
pubmed: 22080603
doi: 10.1104/pp.111.186544
Yin L, et al. U-Net-STN: a novel end-to-end lake boundary prediction model. Land. 2023;12(8):1602.
doi: 10.3390/land12081602