Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)

BMC Genomics

Volumn 19, Issue 1, 2018, Pages

  Visser, Erik A ^a   Wegrzyn, Jill L ^b   Myburg, Alexander A ^a   Naidoo, Sanushka ^a  

^a UNIVERSITY OF PRETORIA   (South Africa)

^b UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Disease resistance; Fusarium circinatum; Pinus patula; Pinus tecunumanii; PR genes; Transcriptome assembly

Indexed keywords

CONTIG; PROTEOME; TRANSCRIPTOME;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; FUSARIUM; FUSARIUM CIRCINATUM; GENE EXPRESSION; GEOGRAPHIC ELEVATION; HOST PATHOGEN INTERACTION; INFECTION RESISTANCE; JUVENILE PLANT; MULTIGENE FAMILY; NONHUMAN; PATHOGENESIS; PINE; PINUS PATULA; PINUS TECUNUMANII; PLANT DEFENSE; PLANT GENE; PLANT TISSUE; SHOOT; TRANSCRIPTOMICS; GENE EXPRESSION PROFILING; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; PHYSIOLOGY; PLANT DISEASE; STANDARD; STANDARDS;

FUSARIUM; GENE EXPRESSION PROFILING; MOLECULAR SEQUENCE ANNOTATION; PINUS; PLANT DISEASES; REFERENCE STANDARDS;

EID: 85052338245     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-018-5015-0     Document Type: Article

References (54)

1. Nirenberg I, O'Donnell K. New Fusarium species and combinations within the Giberella fujikuroi species complex. Mycologia. 1998;90:434-58.
2. Gordon TR, Swett CL, Wingfield MJ. Management of Fusarium diseases affecting conifers. Crop Prot. 2015;73:28-39.
3. Wingfield MJ, Hammerbacher A, Ganley RJ, Steenkamp ET, Gordon TR, Wingfield BD, Coutinho TA. Pitch canker caused by Fusarium circinatum-a growing threat to pine plantations and forests worldwide. Australas Plant Path. 2008;37:319-34.
4. Hodge GR, Dvorak WS. Differential responses of central American and Mexican pine species and Pinus radiata to infection by the pitch canker fungus. New For. 2000;19:241-58.
5. Roux J, Eisenberg B, Kanzler A, Nel A, Coetzee V, Kietzka E, Wingfield MJ. Testing of selected south African Pinus hybrids and families for tolerance to the pitch canker pathogen, Fusarium circinatum. New For. 2007;33:109-23.
6. Mitchell RG, Wingfield MJ, Hodge GR, Steenkamp ET, Coutinho TA. Selection of Pinus spp. in South Africa for tolerance to infection by the pitch canker fungus. New For. 2012;43:473-89.
7. Kanzler A, Nel A, Ford C. Development and commercialisation of the Pinus patula x P. teucnumanii hybrid in response to the threat of Fusarium circinatum. New For. 2014;45:417-37.
8. Tobias PA, Guest DI. Tree immunity: growing old without an immune system. Trends Plant Sci. 2014;19:367-70.
9. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57-63.
10. Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet. 2011;12:671-82.
11. Carrasco A, Wegrzyn JL, Durán R, Fernández M, Donoso A, Rodriguez V, Neale D, Valenzuela S. Expression profiling in Pinus radiata infected with Fusarium circinatum. Tree Genet Genomes. 2017;13:46.
12. Visser EA, Wegrzyn JL, Steenkamp ET, Myburg AA, Naidoo S. Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. BMC Genomics. 2015;16:1057.
13. Macho AP, Zipfel C. Plant PRRs and the activation of innate immune signalling. Mol Cell. 2014;54:263-72.
14. Dangl JL, Jones JDG. Plant pathogens and integrated defence responses to infection. Nature. 2004;411:826-33.
15. Jones JDG, Dangl JL. The plant innate immune system. Nature. 2006;444:323-9.
16. Meng X, Zhang S. MAPK cascades in plant disease resistance signaling. Annu Rev Phytopathol. 2013;51:245-66.
17. Pieterse CMJ, Does DV, Zamioudis C, Leon-Reyes A, Wees SCMV. Hormonal modulation of plant immunity. Annu Rev Cell Dev Bi. 2012;28:489-521.
18. O'Brien JA, Daudi A, Butt VS, Bolwell GP. Reactive oxygen species and their role in plant defence and cell wall metabolism. Planta. 2012;236:765-79.
19. Mengiste T. Plant immunity to necrotrophs. Annu Rev Phytopathol. 2012;50:267-94.
20. Robert-Seilaniantz A, Grant M, Jones JDG. Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annu Rev Phytopathol. 2011;49:317-43.
21. Fu ZQ, Dong X. Systemic acquired resistance: turning local infection into global defence. Annu Rev Plant Biol. 2013;64:839-63.
22. van Loon LC, van Strien EA. The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol. 1999;55:85-97.
23. van Loon LC, Rep M, Pieterse CMJ. Significance of inducible defense-related proteins in infected plants. Annu Rev Phytopathol. 2006;44:135-62.
24. Gamir J, Darwiche R, van't Hof P, Choudhary V, Stumpe M, Scheniter R, Mauch F. The sterol-binding acitivyt of pathogenesis-related protein 1 reveals the mode of action of an antimicrobial protein. Plant J. 2017;89:502-9.
25. Passardi F, Penel C, Dunand C. Performing the paradoxical: how plant peroxidases modify the cell wall. Trends Plant Sci. 2004;9:534-40.
26. Custers JHHV, Harrison SJ, Sela-Buurlage MB, Van Deventer E, Lageweg W, et al. Isolation and characterization of a class of carbohydrate oxidases from higher plants, with a role in active defence. Plant J. 2004;39:147-60.
27. Marcus JP, Goulter KC, Green JL, Harrison SJ, Manners JM. Purification of an antimicrobial peptide from Macadamia integrifolia. Eur J Biochem. 1997;244:743-9.
28. Sooriyaarchchi S, Jaber E, Covarrubias AS, Abhayasekera W, Asiegbu FO, Mowbray SL. Expression and β-glucan binding properties of scots pine (Pinus sylvestris L.) antimicrobial protein (Sp-AMP). Plant Mol Biol. 2011;77:33-45.
29. Andrews S. FastQC a quality control tool for high throughput sequence data. 2012. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
30. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Bruce W, Friedman N, Regev A. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol. 2011;29:644-52.
31. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114-20.
32. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005;21:1859-75.
33. th annual arthropod genomics symposium, Notre Dame; 2013. https://doi.org/10.7490/f1000research.1112594.1 , http://arthropods.eugenes.org/EvidentialGene/about/EvigeneRNA2013poster.pdf.
34. Smith-Unna RD, Boursnell C, Patro R, Hibberd JM, Kelly S. TransRate: reference free quality assessment of de-novo transcriptome assemblies. Genome Res. 2016;26:1134-44.
35. Hart AJ, Ginzburg S, Xu MS, Fisher CR, Rahmatpour N, Mitton JB, Paul R, Wegrzyn JL. EnTAP: bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes: bioRxiv; 2018. p. 307868. https://doi.org/10.1101/307868.
36. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2. Nat Methods. 2012;9:357-9.
37. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:232.
38. Tang S, Lomsadze A, Borodovsky M. GeneMarkS-T: identification of protein coding regions in RNA transcripts. Nucleic Acids Res. 2015;43:e78.
39. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460-1.
40. Buchfink B, Xie C, Huson D. Fast and sensitive protein alignment using diamond. Nat Methods. 2015;12:59-60.
41. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. Eggnog 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;4:D286-93.
42. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210-2.
43. Wegrzyn JL, Lee JM, Tearse BR, Neale DB. TreeGenes: a forest tree genome database. Int J Plant Genomics. 2008;2008:412875.
44. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically inproves orthogroup inference accuracy. Genome Biol. 2015;16:157.
45. Blande D, Halimaa P, Tervahauta AI, Aarts MGM, Kärenlampi SO. De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. Sci Data. 2017;4:160131.
46. Hill CB, Cassin A, Keeble-Gagnère G, Doblin MS, Bacic A, Roessner U. De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. Sci Rep. 2016;6:31558.
47. Fister AS, Mejia LC, Zhang Y, Herre EA, Maximova SN, Guiltinan M. Theobroma cacao. Pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization. BMC Genomics. 2016;17:363.
48. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658-9.
49. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150-2.
50. Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 2014;196:891-909.
51. Pavy N, Pelgas B, Laroche J, Rigault P, Isabel N, Bousquet J. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol. 2012;10:84.
52. Dunwell JM, Gibbings JG, Nahmood T, Saqlan Naqvi SM. Germin and germin-like proteins: evolution, structure, and function. Crit Rev Plant Sci. 2008;27:342-75.
53. Stec B. Plant thionins - the structural perspective. Cell Mol Life Sci. 2006;63:1370-85.
54. Manners JM. Primitive Defence: the MiAMP1 antimicrobial peptide family. Plant Mol Biol Rep. 2009;27:237-42.