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

Show simple item record Visser, Erik A. Wegrzyn, Jill L. Myburg, Alexander Andrew Naidoo, Sanushka 2018-10-25T09:26:28Z 2018-10-25T09:26:28Z 2018-08-23
dc.description Additional file 1: Table S1. RNA-sequencing library statistics. Table S2. Program parameters used for assembly that deviated from the default. Table S3. BUSCO input transcriptome sources. Table S4. OrthoFinder input proteome sources. Table S5. Best hit species distributions. Table S10. Putative PR gene family counts. Table S11. Putative Pinus tecunumanii and Pinus patula PR genes. (XLSX 110 kb) en_ZA
dc.description Additional file 2: Table S6. Pnte_v1.0 annotation. (TSV 48464 kb) en_ZA
dc.description Additional file 3: Table S7. Pipt_v2.0 annotation. (TSV 124607 kb) en_ZA
dc.description Additional file 4: Table S8. Pnte_v1.0 TAIR identifiers. (TSV 2028 kb) en_ZA
dc.description Additional file 5: Table S9. Pipt_v2.0 TAIR identifiers. (TSV 3421 kb) en_ZA
dc.description Additional file 6: Figure S1. Orthologous group distribution across analysed lineages. Secondary and tertiary Venn diagrams were constructed based on the lineage specific orthogroups. (TIFF 2590 kb) en_ZA
dc.description.abstract BACKGROUND : Fusarium circinatum is a pressing threat to the cultivation of many economically important pine tree species. Efforts to develop effective disease management strategies can be aided by investigating the molecular mechanisms involved in the host-pathogen interaction between F. circinatum and pine species. Pinus tecunumanii and Pinus patula are two closely related tropical pine species that differ widely in their resistance to F. circinatum challenge, being resistant and susceptible respectively, providing the potential for a useful pathosystem to investigate the molecular responses underlying resistance to F. circinatum. However, no genomic resources are available for P. tecunumanii. Pathogenesis-related proteins are classes of proteins that play important roles in plant-microbe interactions, e.g. chitinases; proteins that break down the major structural component of fungal cell walls. Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine-F. circinatum interaction. RESULTS : Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula. Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species. CONCLUSIONS : The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying resistance to the pitch canker pathogen, F. circinatum. This study also constitutes, to our knowledge, the largest index of gymnosperm PR-genes to date. en_ZA
dc.description.department Biochemistry en_ZA
dc.description.department Forestry and Agricultural Biotechnology Institute (FABI) en_ZA
dc.description.department Genetics en_ZA
dc.description.department Microbiology and Plant Pathology en_ZA
dc.description.librarian am2018 en_ZA
dc.description.sponsorship The National Research Foundation (NRF) of South Africa Scarce Skills Doctoral Scholarship Programme (Grant ID 97892), the NRF Bioinformatics and Functional Genomics Programme (Grant IDs 86936 and 97911) and a strategic grant from the Department of Science and Technology (DST) for the Tree Genomics Platform at the University of Pretoria. Further support was provided by Sappi, Mondi, York Timbers and Hans Merensky Foundation though the Forest Molecular Genetics (FMG) Programme with co-funding from the Technology and Human Resources for Industry Programme (THRIP, Grant ID 96413). en_ZA
dc.description.uri en_ZA
dc.identifier.citation Visser, E.A., Wegrzyn, J.L., Myburg, A.A. & Naidoo, S. 2018, 'Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)', BMC Genomics, vol. 19, art. 632, pp. 1-13. en_ZA
dc.identifier.issn 1471-2164 (online)
dc.identifier.other 10.1186/s12864-018-5015-0
dc.language.iso en en_ZA
dc.publisher BioMed Central en_ZA
dc.rights © The Author(s). 2018. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( en_ZA
dc.subject Pinus tecunumanii en_ZA
dc.subject Pinus patula en_ZA
dc.subject Transcriptome assembly en_ZA
dc.subject PR genes en_ZA
dc.subject Fusarium circinatum en_ZA
dc.subject Disease resistance en_ZA
dc.title Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation) en_ZA
dc.type Article en_ZA

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