Comparative characterization and expression analysis revealed cinnamyl alcohol dehydrogenase genes differentially responding to Colletotrichum fructicola in woodland and cultivated strawberries
Restricted accessResearch articleFirst published online December 11, 2023
Comparative characterization and expression analysis revealed cinnamyl alcohol dehydrogenase genes differentially responding to Colletotrichum fructicola in woodland and cultivated strawberries
Strawberry (Fragaria×ananassa) production is hampered by anthracnose caused by Colletotrichum spp. Cinnamyl alcohol dehydrogenase (CAD) catalyzes lignin biosynthesis to fortify plant cell wall upon various stresses, but their involvement in strawberry resistance is elusive.
OBJECTIVE:
Current work aims to uncover the involvement of CAD genes in both woodland and cultivated strawberry responses to Colletotrichum spp.
METHODS:
Genome-wide identification of CAD genes was updated in cultivated strawberry. Comparative molecular characterization integrated with pathogenesis phenotyping after C. fructicola inoculation, were followed by RT-qPCR analysis and RNAseq data retrieval.
RESULTS:
Cultivated strawberry comprises 32 CAD genes of three classes. Thirteen syntenic relationships were observed between cultivated and woodland strawberry, with high homology in protein coding regions while promoters being greatly diversified. F. vesca ‘Hawaii4’ was least susceptible, followed by octoploid cultivar ‘ShenQi’, and ‘Benihoppe’ the most susceptible to C. fructicola. The class I CAD4 and CAD5, preferentially expressed in leaves and crowns, respectively, were up-regulated in susceptible varieties at 72 h post inoculation (hpi). Of class II, CAD8 was up-regulated in three genotypes at distinct timepoints, while CAD12 was quickly down-regulated in ‘ShenQi’ upon inoculation. CAD1 and CAD2 of class III were down-regulated in ‘ShenQi’ and ‘Hawaii4’ at distinct stages. The strong involvement of CAD genes in strawberry response to Colletotrichum spp. sets a basis for future functional study.
CONCLUSION:
F. vesca is less susceptible to Colletotrichum spp. than cultivated strawberries but the expression of CAD family in F. vesca and F.×ananassa were differentially provoked in timing and magnitude hinting no correlation with strawberry resistance to this pathogen.
Julián-SánchezA, Riveros-RosasH, PiñaE. In book: Enzymology and Molecular Biology of Carbonyl Metabolism—12 Chapter: Evolution of Cinnamyl Alcohol Dehydrogenase Family. Publisher: Purdue University Press. West Lafayette, Indiana. Editors: H. Weiner, B. Plapp, R. Lindahl, E. Maser. P:142-153.
4.
XuL, ZhuL, TuL, LiuL, YuanD, JinL, LongL, ZhangX. Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. 2011;62(15):5607–21. doi: 10.1093/jxb/err245.
5.
HaileZM, Nagpala-De GuzmanEG, MorettoM, SonegoP, EngelenK, ZoliL, MoserC, BaraldiE. Transcriptome Profiles of Strawberry (Fragaria vesca) Fruit Interacting With Botrytis cinerea at Different Ripening Stages. Front Plant Sci. 2019;10:1131. doi: 10.3389/fpls.2019.01131.
6.
VanholmeR, De MeesterB, RalphJ, BoerjanW. Lignin biosynthesis and its integration into metabolism. Curr Opin Biotechnol. 2019;56:230–239. doi: 10.1016/j.copbio.2019.02.018.
7.
RongW, LuoM, ShanT, WeiX, DuL, XuH, ZhangZ. A Wheat Cinnamyl Alcohol Dehydrogenase TaCAD12 Contributes to Host Resistance to the Sharp Eyespot Disease. Front Plant Sci. 2016;7;1723.. doi: 10.3389/fpls.2016.01723.
8.
LiL, ChengXF, LeshkevichJ, UmezawaT, HardingSA, ChiangVL. The last step of syringyl monolignol biosynthesis in angiosperms is regulated by a novel gene encoding sinapyl alcohol dehydrogenase. Plant Cell. 2001;13(7):1567–86. doi: 10.1105/tpc.010111.
9.
GuoDM, RanJH, WangXQ. Evolution of the Cinnamyl/Sinapyl Alcohol Dehydrogenase (CAD/SAD) gene family: the emergence of real lignin is associated with the origin of Bona Fide CAD. J Mol Evol. 2010;71(3):202–18. doi: 10.1007/s00239-010-9378-3.
10.
YanX, LiuJ, KimH, LiuB, HuangX, YangZ, LinY-CJ, ChenH, YangC, WangJPet al. , CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa. New Phytol. 2019;222:244–260. doi: 10.1111/nph.15505.
11.
BarakatA, Bagniewska-ZadwornaA, ChoiA, PlakkatU, DiLoretoDS, YellankiP, CarlsonJE. The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression. BMC Plant Biol. 2009;9:26. doi: 10.1186/1471-2229-9-26.
12.
de VriesJ, de VriesS, SlamovitsCH, RoseLE & ArchibaldJM. How embryophytic is the biosynthesis of phenylpropanoids and their derivatives in streptophyte algae?Plant and Cell Physiology. 2017;58(5):934–945. doi: 10.1093/pcp/pcx037.
13.
JiangS, TianX, HuangX, XinJ, YanH. Physcomitrium patens CAD1 has distinct roles in growth and resistance to biotic stress. BMC Plant Biology. 2022;22(1):518. doi: 10.1186/s12870-022-03892-3.
14.
SaballosA, EjetaG, SanchezE, KangC, VermerrisW. A genomewide analysis of the cinnamyl alcohol dehydrogenase family in sorghum [Sorghum bicolor (L.) Moench] identifies SbCAD2 as the brown midrib6 gene. Genetics. 2009;181(2):783–95. doi: 10.1534/genetics.108.098996.
15.
de VriesS, Fürst-JansenJMR, IrisarriI, et al. The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families. Plant J. 2021;107(4):975–1002.
16.
SiboutR, EudesA, MouilleG, PolletB, LapierreC, JouaninL, SéguinA. CINNAMYL ALCOHOL DEHYDROGENASE-C and -D are theprimary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell. 2005;17(7):2059–76. doi: 10.1105/tpc.105.030767.
17.
KimSJ, KimKW, ChoMH, FranceschiVR, DavinLB, LewisNG. Expression of cinnamyl alcohol dehydrogenases and their putative homologues during Arabidopsis thaliana growth and development: lessons for database annotations?Phytochemistry. 2007;68(14):1957–74. doi: 10.1016/j.phytochem.2007.02.032.
18.
KiedrowskiS, KawalleckP, HahlbrockK, SomssichIE, DanglJL. Rapid activation of a novel plant defense gene is strictly dependent on the Arabidopsis RPM1 disease resistance locus. EMBO J. 1992;11(13):4677–84. doi: 10.1002/j.1460-2075.1992.tb05572.x.
19.
SattlerSE, SaathoffAJ, HaasEJ, PalmerNA, Funnell-HarrisDL, SarathG, PedersenJF. A nonsense mutation in a cinnamyl alcohol dehydrogenase gene is responsible for the Sorghum brown midrib6 phenotype. Plant Physiol. 2009;150(2):584–95. doi: 10.1104/pp.109.136408.
20.
MaQH. Functional analysis of a cinnamyl alcohol dehydrogenase involved in lignin biosynthesis in wheat. J Exp Bot. 2010;61(10):2735–44. doi: 10.1093/jxb/erq107.
21.
HiranoK, AyaK, KondoM, OkunoA, MorinakaY, & MatsuokaM. OsCAD2 is the major CAD gene responsible for monolignol biosynthesis in rice culm. Plant Cell Reports. 2011;31(1):91–101. doi: 10.1007/s00299-011-1142-7.
22.
DengWW, ZhangM, WuJQ, JiangZZ, TangL, LiYY, WeiCL, JiangCJ, WanXC. Molecular cloning, functional analysis of three cinnamyl alcohol dehydrogenase (CAD) genes in the leaves of tea plant, Camellia sinensis. J Plant Physiol. 2013;170(3):272–82. doi: 10.1016/j.jplph.2012.10.010.
23.
Bagniewska-ZadwornaA, BarakatA, LakomyP, SmolińskiDJ, ZadwornyM. Lignin and lignans in plant defence: insight from expression profiling of cinnamyl alcohol dehydrogenase genes during development and following fungal infection in Populus. Plant Sci. 2014;229:111–121. doi: 10.1016/j.plantsci.2014.08.015.
24.
JinY, ZhangC, LiuW, QiH, ChenH, CaoS. The cinnamyl alcohol dehydrogenase gene family in melon (Cucumis melo L.): bioinformatic analysis and expression patterns. PLoS One. 2014;9(7):e101730. doi: 10.1371/journal.pone.0101730.
25.
LiH, ZhangS, ZhaoY, ZhaoX, XieW, GuoY, WangY, LiK, GuoJ, ZhuQ-H, ZhangX, JiaK-P and MiaoY. Identification and Characterization of Cinnamyl Alcohol Dehydrogenase Encoding Genes Involved in Lignin Biosynthesis and Resistance to Verticillium dahliae in Upland Cotton (Gossypium hirsutum L.). Front Plant Sci. 2022;13:840397. doi: 10.3389/fpls.2022.840397.
26.
TronchetM, BalaguéC, KrojT, JouaninL, RobyD. Cinnamylalcohol dehydrogenases-C and D, key enzymes in lignin biosynthesis,play an essential role in disease resistance in Arabidopsis. MolPlant Pathol. 2010;11(1):83–92. 10.1111/j.1364-3703.2009
27.
LiT, WangQ, FengR, LiL, DingL, FanG, LiW, DuY, ZhangM, HuangG, SchäferP, MengY, TylerBM, ShanW. Negative regulators of plant immunity derived from cinnamyl alcohol dehydrogenases are targeted by multiple Phytophthora Avr3a-like effectors. New Phytol. 2019; 10.1111/nph.16139. doi: 10.1111/nph.16139.
28.
HardiganMA, LorantA, PincotDDA, FeldmannMJ, FamulaRA, AcharyaCB, LeeS, VermaS, WhitakerVM, BassilN, ZurnJ, ColeGS, BirdK, EdgerPP, KnappSJ. Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry. Mol Biol Evol. 2021;38(6):2285–2305. doi: 10.1093/molbev/msab024.
LiY, PiM, GaoQ, LiuZ, KangC. Updated annotation of the wild strawberry Fragaria vesca V4 genome. Horticulture Research. 2019;6:61–61. doi: 10.1038/s41438-019-0142-6.
31.
LiuT, LiM, LiuZ, AiX, LiY. Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. Horticulture Research. 2021;8(1):41–41. doi: 10.1038/s41438-021-00476-4.
32.
HowardCM, MaasJL, ChandlerCL, & AlbregtsEA. Anthracnose of strawberry caused by the Colletotrichum complex in Florida. Plant Disease. 1992;76:976–981. doi: 10.1094/PD-76-0976.
33.
ShaoX. New disease of strawberry: strawberry anthracnose. Acta Agric Shanghai. 1992;8(2):86–7. (in Chinese).
34.
AdhikariTB, ChaconJG, FernandezGE, LouwsFJ. First report of anthracnose causing both crown and fruit rot of strawberry by Colletotrichum siamense in North Carolina. Plant Dis. 2019;103:1775. doi: 10.1094/pdis-02-19-0314-pdn.
35.
HuS, ZhangY, YuH, ZhouJ, HuM, LiuA, WuJ, WangH, ZhangC. Colletotrichum spp. Diversity Between Leaf Anthracnose and Crown Rot from the Same Strawberry Plant. Front. Microbiol. 2022;3:860694. doi: 10.3389/fmicb.2022.860694.
36.
JiY, LiX, GaoQ-H, GengC, DuanK. Colletotrichum species pathogenic to strawberry: discovery history, global diversity, prevalence in China, and the host range of top two species. Phytopathology Research. 2022;4:42. doi.org/10.1186/s42483-022-00147-9.
37.
OliveiraMS, WangNY, PeresNA. Multilocus phylogenetic analyses of Colletotrichum gloeosporioides species complex causing crown rot on strawberry in Florida. Phytopathology. 2022;112(4):898–906. doi.org/10.1094/PHYTO-04-20-0151-R.
38.
WuJY, HuXR, ZhangCQ. Molecular detection of QoI resistance in Colletotrichum gloeosporioides causing strawberry anthracnose based on loop-mediated isothermal amplification assay. Plant Dis. 2019;103:1319–1325. doi: 10.1094/PDIS-09-18-1593-RE.
39.
WangP, YangJ, LiZY, ZhuJJ, GaoQH, NiDA, DuanK. Genome-wide identification and expression analysis revealed cinnamyl alcohol dehydrogenase genes correlated with fruit-firmness in strawberry. Journal of Berry Research. 2021;11(3):447–464. doi: 10.3233/jbr-210729.
40.
ZhangL, HuangX, HeC, ZhangQY, ZouX, DuanK, GaoQ. Novel Fungal Pathogenicity and Leaf Defense Strategies Are Revealed by Simultaneous Transcriptome Analysis of Colletotrichum fructicola and Strawberry Infected by This Fungus. Front Plant Sci. 2018;9:434. doi: 10.3389/fpls.2018.00434.
41.
JinB-C, ZhangL, XingD-M, ZhangG-Z. Disease occurrence and resistance of 11 strawberry cultivars to anthracnose in the field. Plant Protection. 2014;40(02):123–126+131. (in Chinese).
42.
ChenC, ChenH, ZhangY, ThomasHR, FrankMH, HeY, XiaR. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol. Plant. 2020;13:1194–1202. doi: 10.1016/j.molp.2020.06.009.
43.
RobertX, GouetP. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research. 2014;42(W1):W320–W324. doi: 10.1093/nar/gku316.
44.
VoorripsRE. MapChart: Software for the graphical presentation of linkage maps and QTLs. J. Hered. 2002;93:77–78. doi: 10.1093/jhered/93.1.77.
45.
TangH, BowersJE, WangX, MingR, AlamM, PatersonAH. Synteny and collinearity in plant genomes. Science. 2008;320(5875):486–8. doi: 10.1126/science.1153917.
46.
BaiY, LiZ, ZhuJ, ChenS, DongC, GaoQ, DuanK. Unraveling NPR-like Family Genes in Fragaria spp. Facilitated to Identify Putative NPR1 and NPR3/4 Orthologues Participating in Strawberry-Colletotrichum fructicola Interaction. Plants (Basel). 2022;11(12):1589. doi: 10.3390/plants11121589.
47.
Amil-RuizF, Garrido-GalaJ, Blanco-PortalesR, FoltaKM, Muñoz-BlancoJ, CaballeroJL. Identification and validation of reference genes for transcript normalization in strawberry (Fragaria×ananassa) defense responses. PloS One. 2013;8(8):e70603–e70603. doi: 10.1371/journal.pone.0070603.
48.
WangF, ZhangF, ChenM, LiuZ, ZhangZ, FuJ, MaY. Comparative Transcriptomics Reveals Differential Gene Expression Related to Colletotrichum gloeosporioides Resistance in the Octoploid Strawberry. Front Plant Sci. 2017;8:779. doi: 10.3389/fpls.2017.00779.
49.
ChandraS, OhY, HanH, SalinasN, AnciroA, WhitakerVM, ChaconJG, FernandezG, LeeS. Comparative Transcriptome Analysis to Identify Candidate Genes for FaRCg1 Conferring Resistance Against Colletotrichum gloeosporioides in Cultivated Strawberry (Fragaria×ananassa). Front Genet. 2021;12:730444. doi: 10.3389/fgene.2021.730444.
50.
AdhikariTB, AryalR, RedpathLE, Van den BroeckL, AshrafiH, PhilbrickAN, JacobsRL, SozzaniR, LouwsFJ. RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry. Front. Genet. 2022;12:805771. doi: 10.3389/fgene.2021.805771.
51.
KimSJ, KimMR, BedgarDL, MoinuddinSG, CardenasCL, DavinLB, KangC, LewisNG. Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. Proc Natl Acad Sci U S A. 2004;101(6):1455–60. doi: 10.1073/pnas.0307987100.
52.
BustinSA, BenesV, GarsonJA, HellemansJ, HuggettJ, KubistaM, MuellerR, NolanT, PfafflMW, ShipleyGL. The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clinical Chemistry. 2009;55(4):611–22. doi: 10.1373/clinchem.2008.112797.
53.
PincotDDA, LeddaM, FeldmannMJ, HardiganMA, PoortenTJ, RuncieDE, HeffelfingerC, DellaportaSL, ColeGS, KnappSJ. Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3 (Bethesda). 2021;11(3):jkab015. doi: 10.1093/g3journal/jkab015.
54.
HanY-C, ZengX-G, XiangF-Y, GuoC, ZhangQ-H, ChenF-Y, GuanW. In vitro evaluation of the resistance of strawberry germplasm resources to anthracnoid. Scientia Agriculturae Sinica. 2019;52(20):3585–3594. (in Chinese).
55.
Amil-RuizF, Blanco-PortalesR, Muñoz-BlancoJ, CaballeroJL. The strawberry plant defense mechanism: a molecular review. Plant Cell Physiol. 2011;52(11):1873–903. doi: 10.1093/pcp/pcr136.
56.
MottiarY, VanholmeR, BoerjanW, RalphJ, MansfieldSD. Designer lignins: Harnessing the plasticity of lignification. Curr Opin Biotechnol. 2016;37:190–200. doi: 10.1016/j.copbio.2015.10.009.
57.
SiboutR, EudesA, PolletB, GoujonT, MilaI, GranierF, SeguinA, LapierreC, JouaninL. Expression pattern of two paralogs encoding cinnamyl alcohol dehydrogenases in Arabidopsis. Isolation and characterization of the corresponding mutants. Plant Physiol. 2003;132(2):848–60. doi: 10.1104/pp.103.021048.
58.
NovakovskiyR, PovkhovaL, KrasnovGS, RozhminaTA, ZhuchenkoAA, KudryavtsevaLP, et al. The cinnamyl alcohol dehydrogenase gene family is involved in the response to Fusarium oxysporum in resistant and susceptible flax genotypes. Vavilov Journal of Genetics and Breeding. 2019;23(7):896–901. doi: 10.18699/VJ19.564.
59.
LiN, LinB, WangH, LiX, YangF, DingX, ChuZ. Natural variation in ZmFBL41 confers banded leaf and sheath blight resistance in maize. Nature Genetics. 2019;51(10):1540–1548. doi: 10.1038/s41588-019-0503-y.
60.
ZhangL, SongL, XuX, ZouX, DuanK, GaoQ. Characterization and Fungicide Sensitivity of Colletotrichum Species Causing Strawberry Anthracnose in Eastern China. Plant Dis. 2020;104(7):1960–1968. doi: 10.1094/PDIS-10-19-2241-RE.
61.
Gallego-GiraldoL, JikumaruY, KamiyaY, TangY, DixonRA. Selective lignin downregulation leads to constitutive defense response expression in alfalfa (Medicago sativa L.). New Phytol. 2011;190(3):627–639. doi: 10.1111/j.1469-8137.2010.03621.x.
62.
WanJ, HeM, HouQ, ZouL, YangY, WeiY, ChenX. Cell wall associated immunity in plants. Stress Biology. 2021;1(1). doi: 10.1007/s44154-021-00003-4.
ChenC, ChangJ, WangS, LuJ, LiuY, SiH, MaC. Cloning, expression analysis and molecular marker development of cinnamyl alcohol dehydrogenase gene in common wheat. Protoplasma. 2021;258(4):881–889. doi: 10.1007/s00709-021-01607-3.
65.
Morita-YamamuroC, TsutsuiT, SatoM, YoshiokaH, TamaokiM, OgawaD, MatsuuraH, YoshiharaT, IkedaA, UyedaI, YamaguchiJ. The Arabidopsis gene CAD1 controls programmed cell death in the plant immune system and encodes a protein containing a MACPF domain. Plant Cell Physiol. 2005;46(6):902–12. doi: 10.1093/pcp/pci095.
66.
EudesA, PolletB, SiboutR, DoCT, SeguinA, LapierreC, JouaninL. Evidence for a role of AtCAD1 in lignification of elongating stems of Arabidopsis thaliana. Planta. 2006;225(1):23–39. doi: 10.1007/s00425-006-0326-9.
