Arenhart R A, Bai Y, de Oliveira L F V, Neto L B, Schunemann M, Maraschin F S, Mariath J, Silverio A, Sachetto-Martins G, Margis R, Wang Z Y, Margis-Pinheiro M. 2013. New insights into aluminum tolerance in rice: The ASR5 protein binds the STAR1 promoter and other aluminum-responsive genes. Molecular Plant, 7, 709–721.
Basu D, Haswell E S. 2020. The mechanosensitive ion channel MSL10 potentiates responses to cell swelling in Arabidopsis seedlings. Current Biology, 30, 2716–2728.
Cakir B, Agasse A, Gaillard C, Saumonneau A, Delrot S, Atanassova R. 2003. A grape ASR protein involved in sugar and abscisic acid signaling. The Plant Cell, 15, 2165–2180.
Cheng Z C, Zhao H H, Li J L, Zhang C S, Wang F L. 2012. Identification of tobacco-parasitizing cyst nematode and intrapopulation rDNA-ITS-RFLP analysis in Shandong province. Acta Phytopathologica Sinica, 42, 387–395. (in Chinese)
Daykin M E, Hussey H S. 1985. Staining and histopathological techniques in nematology. In: Barker K R, Carter C C, Sasser J N, eds., An Advanced Treatise on Meloidogyne: Methodology, vol II. North Carolina State University Graphics, Raleigh. pp. 39–48.
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G. 2012. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature, 485, 201–206.
Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim M S, Dai Q, Segni A D, Salmon-Divon M, Clark W C, Zheng G Q, Pan T, Solomon O, Eyal E, Hershkovitz V, Han D L, Doré L C, Amariglio N, Rechavi G, He C. 2016. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature, 530, 441–446.
Dong X, Hong Z, Chatterjee J, Kim S, Verma D. 2008. Expression of callose synthase genes and its connection with NPR1 signaling pathway during pathogen infection. Planta, 229, 87–98.
Duan H C, Wei L H, Zhang C, Wang Y, Chen L, Lu Z, Chen P R, He C, Jia G F. 2017. ALKBH10B Is an RNA N6-methyladenosine demethylase affecting Arabidopsis floral transition. The Plant Cell, 29, 2995–3011.
Dufresne M, Bailey J A, Dron M, Langin T. 1998. clk1, a serine/threonine protein kinase-encoding gene, is involved in pathogenicity of Colletotrichum lindemuthianum on common bean. Molecular Plant-Microbe Interactions, 11, 99–108.
Durrant W E, Rowland O, Piedras P, Hammond-Kosack K E, Jones J D G. 2000. cDNA-AFLP reveals a striking overlap in race specific resistance and wound response gene expression profiles. The Plant Cell, 12, 963–977.
Ge C X, Tang C X, Zhu Y X, Wang G F. 2021. Genome-wide identification of the maize 2OGD superfamily genes and their response to Fusarium verticillioides and Fusarium graminearum. Gene, 764, 145078.
Gillet F X, Bournaud C, Antonino D S J J D, Grossi-De-Sa M F. 2017. Plantparasitic nematodes: Towards understanding molecular players in stress responses. Annals of Botany, 119, 775–789.
Govindan G, Sharma B, Li Y F, Armstrong C D, Merum P, Rohila J S, Gregory B D, Sunkar R. 2022. mRNA N6-methyladenosine is critical for cold tolerance in Arabidopsis. Plant Journal, 111, 1052–1068.
Gu Y Q, Wildermuth M C, Chakravarthy S, Loh Y T, Yang C M, He X H, Han Y, Martin G B. 2002. Tomato transcription factors Pti4, Pti5, and Pti6 activate defense responses when expressed in Arabidopsis. The Plant Cell, 14, 817–831.
Guo X L, Chronis D, Torre C M D L, Smeda J, Wang X H, Mitchum M G. 2015. Enhanced resistance to soybean cyst nematode Heterodera glycines in transgenic soybean by silencing putative CLE receptors. Plant Biotechnology Journal, 13, 801–810.
Han X, Shi Q Q, He Z Y, Song W W, Chen Q S, Qi Z M. 2022. Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection. aBIOTECH, 3, 197–211.
Han X, Wang J L, Zhang Y, Kong Y L, Dong H Y, Feng X Z, Li T S, Zhou C J, Yu J D, Xin D W, Chen Q S, Qi Z M. 2023. Changes in the m6A RNA methylome accompany the promotion of soybean root growth by rhizobia under cadmium stress. Journal of Hazardous Materials, 441, 129843.
He P C, Wei J B, Dou X Y, Harada B T, Zhang Z J, Ge R Q, Liu C, Zhang L S, Yu X B, Wang S, Lyu R T, Zou Z Y, Chen M J, He C. 2023. Exon architecture controls mRNA m6A suppression and gene expression. Science, 379, 677–682.
He Y J, Li L L, Yao Y X, Li Y L, Zhang H Q, Fan M. 2021. Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection. BMC Plant Biology, 21, 516.
Heinz S, Benner C, Spann N, Bertolino E, Lin Y C, Laslo P, Cheng J X, Murre C, Singh H, Glass C K. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular Cell, 38, 576–589.
Hou Y F, Sun J, Wu B X, Gao Y Y, Nie H B, Nie Z T, Quan S X, Wang Y, Cao X F, Li S S. 2021. CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis. Molecular Plant, 14, 688–699.
Hu J Z, Cai J, Park S J, Lee K, Li Y X, Chen Y, Yun J Y, Xu T, Kang H S. 2021. N6-Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. Plant Journal, 106, 1759–1775.
Huang M H, Jiang Y, Qin R F, Jiang D, Chang D D, Tian Z Y, Li C J, Wang C L. 2022. Full-length transcriptional analysis of the same soybean genotype with compatible and incompatible reactions to Heterodera glycines reveals nematode infection activating plant defense response. Fronters in Plant Science, 13, 866322.
Jeyaraj A, Wang X W, Wang S S, Liu S R, Zhang R, Wu A, Wei C L. 2019. Identification of regulatory networks of microRNAs and their targets in response to Colletotrichum gloeosporioides in tea plant (Camellia sinensis L). Frontiers in Plant Science, 10, 1096.
Kammerhofer N, Radakovic Z, Regis J M A, Dobrev P, Vankova R, Grundler F M W, Siddique S, Hofmann J, Wieczorek K. 2015. Role of stress-related hormones in plant defence during early infection of the cyst nematode Heterodera schachtii in Arabidopsis. New Phytologist, 207, 778–789.
Klink V P, Overall C C, Alkharouf N W, MacDonald M H, Matthews B F. 2007. A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection. Planta, 226, 1423–1447.
Ko J H, Yang S H, Han K H. 2006. Upregulation of an Arabidopsis RING-H2 gene, XERICO, confers drought tolerance through increased abscisic acid biosynthesis. Plant Journal, 47, 343–355.
Koiwai H, Tagiri A, Katoh S, Katoh E, Ichikawa H, Minami E, Nishizawa Y. 2007. RING-H2 type ubiquitin ligase EL5 is involved in root development through the maintenance of cell viability in rice. Plant Journal, 51, 92–104.
Krishnan A, Chidambareswaren M, Tomson M, Manjula S. 2015. Virus-induced gene silencing (VIGS) for elucidation of pathogen defense role of serine/threonine protein kinase in the non-model plant Piper colubrinum link. The Plant Cell Tissue and Organ Culture, 122, 269–283.
Li B, Wang X, Li Z, Lu C, Zhang Q, Chang L, Li W, Cheng T, Xia Q, Zhao P. 2019. Transcriptome-wide analysis of N6-methyladenosine uncovers its regulatory role in gene expression in the lepidopteran Bombyx mori. Insect Molecular Biology, 28, 703–715.
Li S, Chen Y, Zhu X, Wang Y, Jung K H, Chen L, Xuan Y H, Duan Y X. 2018. The transcriptomic changes of Huipizhi Heidou (Glycine max), a nematode resistant black soybean during Heterodera glycines race 3 infection. Plant Physiology, 220, 96–104.
Liang Z, Geng Y, Gu X. 2018. Adenine methylation: New epigenetic marker of DNA and mRNA. Molecular Plant, 11, 1219–1221.
Liu H Q, Liu Q C, Zhao H H. 2016. Comparative analysis of the parasitism between soybean and tobacco populations of Heterodera glycines. Plant Protection, 42, 68–73. (in Chinese)
Liu H Y, Dai J R, Feng D R, Liu B, Wang H B, Wang J F. 2010. Characterization of a novel plantain Asr gene, MpAsr, that is regulated in response to infection of Fusarium oxysporum f. sp. cubense and abiotic stresses. Journal of Integrative Plant Biology, 52, 315–323.
Liu H Z, Zhang H J, Yang Y Y, Li G J, Yang Y X, Wang X E, Basnayake B M V S, Li D Y, Song F M. 2008. Functional analysis reveals pleiotropic effects of rice RING-H2 finger protein gene OsBIRF1 on regulation of growth and defense responses against abiotic and biotic stresses. Plant Molecular Biology, 68, 17–30.
Liu Q, Mu B J, Meng Y J, Yu L M, Wang Z R, Jia T, Zheng W B, Gao W W, Xie S C, Zhu X Q. 2023. New insights into developmental biology of Eimeria tenella revealed by comparative analysis of mRNA N6-methyladenosine modifications between unsporulated oocysts and sporulated oocysts. Journal of Integrative Agriculture, 23, 239–250.
Liu S M, Kandoth P K, Warren S D, Yeckel G, Heinz R, Alden J, Yang C L, Jamai A, El-Mellouki T, Juvale P S, Hill J, Baum T J, Cianzio S, Whitham S A, Korkin D, Mitchum M G, Meksem K. 2012. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature, 492, 256–260.
Liu Z, Zhang L P, Zhao J, Jian J Z, Peng H, Huang W K, Kong L A, Peng D L, Liu S M. 2022. A fragment of a 70-kDa Heterodera glycines heat shock protein (HgHSP70) interacts with soybean cyst nematode-resistant GmSHMT08. Journal of Integrative Agriculture, 21, 2973–2983.
Livak K J, Schmittgen T D. 2002. Analysis of relative gene expression data using real-time quantitative PCR. Methods, 25, 402–408.
Luo H, Song F, Goodman R M, Zheng Z. 2005. Up-regulation of OsBIHD1, a rice gene encoding BELL homeodomain transcriptional factor, in disease resistance responses. Plant Biology, 7, 459–468.
Luo X M, Wu W, Liang Y B, Xu N, Wang Z Y, Zou H S, Liu J. 2020. Tyrosine phosphorylation of the lectin receptor-like kinase LORE regulates plant immunity. The EMBO Journal, 39, e102856.
Maldonado A, Youssef R, Mcdonald M, Brewer E, Beard H, Matthews B. 2014. Overexpression of four Arabidopsis thaliana NHL genes in soybean (Glycine max) roots and their effect on resistance to the soybean cyst nematode (Heterodera glycines). Physiological and Molecular Plant Pathology, 86, 1–10.
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet Journal, 17, 10–12.
Martínez-Pérez M, Aparicio F, López-Gresa M P, Bellés J M, Sánchez-Navarro J A, Pallás V. 2017. Arabidopsis m6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs. Proceedings of the National Academy of Sciences of the United States of America, 114, 10755–10760.
McNeece B T, Sharma K, Lawrence G W, Lawrence K S, Klink V P. 2019. The mitogen activated protein kinase (MAPK) gene family functions as a cohort during the Glycine max defense response to Heterodera glycines. Plant Physiology and Biochemistry, 137, 25–41.
Melillo M T, Leonetti P, Bongiovanni M, Castagnone-Sereno P, Bleve-Zacheo T. 2006. Modulation of reactive oxygen species activities and H2O2 accumulation during compatible and incompatible tomato-root-knot nematode interactions. New Phytologist, 170, 501–512.
Meng J, Lu Z L, Liu H, Zhang L, Zhang S W, Chen Y D, Rao M K, Huang Y F. 2014. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. Methods, 69, 274–281.
Miao Z Y, Zhang T, Qi Y H, Song J, Han Z X, Ma C. 2020. Evolution of the RNA N6-methyladenosine methylome mediated by genomic duplication. Plant Physiology, 182, 345–360.
Miraeiz E, Chaiprom U, Afsharifar A, Karegar A, Drnevich J M, Hudson M E. 2020. Early transcriptional responses to soybean cyst nematode HG Type 0 show genetic differences among resistant and susceptible soybeans. Theoretical and Applied Genetics, 133, 87–102.
Mondo S J, Dannebaum R O, Kuo R C, Louie K B, Bewick A J, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt S R, Lau R, Bowen B P, Lipzen A, Sullivan W, Andreopoulos B B, Clum A, Lindquist E, Daum C, Northen T R, Kunde-Ramamoorthy G, et al. 2017. Widespread adenine N6-methylation of active genes in fungi. Nature Genetics, 49, 964–968.
Nishimura M T, Stein M, Hou B H, Vogel J P, Edwards H, Somerville S C. 2003. Loss of a callose synthase results in salicylic acid-dependent disease resistance. Science, 301, 969–972.
Pertea M, Pertea G M, Antonescu C M, Chang T C, Mendell J T, Salzberg S L. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33, 290–295.
Rambani A J, Hu Y F, Piya S, Long M, Rice J H, Pantalone V, Hewezi T. 2020a. Identification of differentially methylated miRNA genes during compatible and incompatible interactions between soybean and soybean cyst nematode. Molecular Plant–Microbe Interactions, 33, 1340–1352.
Rambani A J, Pantalone V, Yang S N, Rice J H, Song Q J, Mazarei M, Arelli P R, Meksem K, Stewart C N, Hewezi T. 2020b. Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism. New Phytologist, 227, 168–184.
Rambani A J, Rice J H, Liu J Y, Lane T, Ranjan P, Mazarei M, Pantalone V, Stewart C N J, Staton M, Hewezi T. 2015. The methylome of soybean roots during the compatible interaction with the soybean cyst nematode. Plant Physiology, 168, 1364–1377.
Redding N W, Paula A, Christina E W. 2018. Multiple nodulation genes are up-regulated during establishment of reniform nematode feeding sites in soybean. Phytopathology, 108, 275–291.
Robinson M D, McCarthy D J, Smyth G K. 2010. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139–140.
Shaibu A S, Li B, Zhang S R, Sun J M. 2020. Soybean cyst nematode-resistance: Gene identification and breeding strategies. The Crop Journal, 8, 892–904.
Shao Y, Wong C E, Shen L, Yu H. 2021. N6-methyladenosine modification underlies messenger RNA metabolism and plant development. Current Opinion in Plant Biology, 63, 102047.
Smirnova E, Marquis V, Poirier L, Aubert Y, Zumsteg J M R, Miesch L, Heitz T. 2017. Jasmonic acid oxidase 2 hydroxylates jasmonic acid and represses basal defense and resistance responses against Botrytis cinerea infection. Molecular Plant, 10, 1159–1173.
Song W W, Qi N W, Liang C, Duan F M, Zhao H H. 2019. Soybean root transcriptome profiling reveals a nonhost resistant response during Heterodera glycines infection. PLoS ONE, 14, e0217130.
Squires J E, Patel H R, Nousch M, Sibbritt T, Humphreys D T, Parker B J, Suter C M, Preiss T. 2012. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Research, 40, 5023–5033.
Su T T, Fu L B, Kuang L H, Chen D Y, Zhang G P, Shen Q F, Wu D Z. 2022. Transcriptome-wide m6A methylation profile reveals regulatory networks in roots of barley under cadmium stress. Journal of Hazardous Materials, 423, 127140.
Tang J, Chen S Y, Jia G F. 2023. Detection, regulation, and functions of RNA N6-methyladenosine modification in plants. Plant Communications, 4, 100546.
Wan Y Z, Tang K, Zhang D Y, Xie S J, Zhu X H, Wang Z G, Lang Z B. 2015. Transcriptome-wide high-throughput deep m6A-seq reveals unique differential m6A methylation patterns between three organs in Arabidopsis thaliana. Genome Biology, 16, 272.
Wang C L, Yang J B, Song P Z, Zhang W, Lu Q, Yu Q, Jia G F. 2022. FIONA1 is an RNA N6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering. Genome Biology, 31, 40.
Wang H M, Zhao H H, Wang F L. 2014. Morphological variation of Heterodera glycines from different hosts and their adaptability to soybean. Plant Protection, 40, 106–111. (in Chinese)
Wang N, Peng H, Liu S M, Huang W K, Holgado R, Liu-Clarke J H, Peng D L. 2019. Molecular characterization and functional analysis of two new lysozyme genes from soybean cyst nematode (Heterodera glycines). Journal of Integrative Agriculture, 18, 2806–2813.
Wei L H, Song P Z, Wang Y, Lu Z K, Tang Q, Yu Q, Xiao Y, Zhang X, Duan H C, Jia G F. 2018. The m6A reader ECT2 controls trichome morphology by affecting mRNA stability in Arabidopsis. The Plant Cell, 30, 968–985.
Xiao W, Adhikari S, Dahal U, Chen Y S, Hao Y J, Sun B F, Sun H Y, Li A, Ping X L, Lai W Y, Wang X, Ma H L, Huang C M, Yang Y, Huang N, Jiang G B, Wang H L, Zhou Q, Wang X J, Zhao Y L, Yang Y G. 2016. Nuclear m6A reader YTHDC1 regulates mRNA splicing. Molecular Cell, 61, 507–519.
Xin X F, Nomura K, Ding X H, Chen X J, Wang K, Aung K, Uribe F, Rosa B, Yao J, Chen J, He S Y. 2015. Pseudomonas syringae effector avirulence protein E localizes to the host plasma membrane and down-regulates the expression of the NONRACE-SPECIFIC DISEASE RESISTANCE1/HARPIN-INDUCED1-LIKE13 gene required for antibacterial immunity in Arabidopsis. Plant Physiology, 169, 793–802.
Xu Z H, Shi X B, Bao M M, Song X Q, Zhang Y X, Wang H Y, Xie H R, Mao F, Wang S, Jin H M, Dong S M, Zhang F, Wu Z, Wu Y F. 2021. Transcriptome-wide analysis of RNA m6A methylation and gene expression changes among two Arabidopsis ecotypes and their reciprocal hybrids. Frontiers in Plant Science, 12, 685189.
Yang C Y, Chen Y C, Jauh G Y, Wang C S. 2005. A Lily ASR protein involves abscisic acid signaling and confers drought and salt resistance in Arabidopsis. Plant Physiology, 139, 836–846.
Yang X, Triboulet R, Liu Q, Sendinc E, Gregory R I. 2022. Exon junction complex shapes the m6A epitranscriptome. Nature Communication, 13, 7904.
Yu G C, Wang L G, He Q Y. 2015. ChIPseeker: An R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics, 31, 2382–2383.
Yue H, Nie X J, Yan Z G, Song W N. 2019. N6-methyladenosine regulatory machinery in plants: Composition, function and evolution. Plant Biotechnology Journal, 17, 1194–1208.
Zhang F, Zhang Y C, Liao J Y, Yu Y, Zhou Y F, Feng Y Z, Yang Y W, Lei M Q, Bai M, Wu H, Chen Y Q. 2019. The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice. PLoS Genetics, 15, e1008120.
Zhang H M, Deng X Y, Miki D, Cutler S, La H G, Hou Y J, Oh J E, Zhu J K. 2012. Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis. The Plant Cell, 24, 1230–1241.
Zhang H X, Li F F, Li Z Z, Cheng J, Chen X K, Wang Q H, Joosten M H A J, Shan W X, Du Y. 2021. Potato StMPK7 is a downstream component of StMKK1 and promotes resistance to the oomycete pathogen Phytophthora infestans. Molecular Plant Pathology, 22, 644–657.
Zhang K, Zhuang X J, Dong Z Z, Xu K, Chen X J, Liu F, Zhen H. 2021. The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses. Genome Biology, 22, 189.
Zhang T Y, Wang Z Q, Hu H C, Chen Z Q, Liu P, Gao S Q, Zhang F, He L, Jin P, Xu M Z, Chen J P, Yang J. 2021. Transcriptome-wide N6-methyladenosine (m6A) profiling of susceptible and resistant wheat varieties reveals the involvement of variety-specific m6A modification involved in virus-host interaction pathways. Frontiers in Microbiology, 12, 656302.
Zhao M W, Ge Y, Xu Z Y, Ouyang X, Jia Y L, Liu J T, Zhang M X, An Y Y. 2022. A BTB/POZ domain-containing protein negatively regulates plant immunity in Nicotiana benthamiana. Biochemical and Biophysical Research Communications, 600, 54–59.
Zhou L, Tian S, Qin G. 2019. RNA methylomes reveal the m6A mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening. Genome Biology, 20, 156.
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