Coniochaeta endophytica sp. nov., a foliar endophyte associated with healthy photosynthetic tissue of Platycladus orientalis (Cupressaceae)

Abstract

The ecologically diverse genus Coniochaeta (Coniochaetaceae, Ascomycota) contains numerous endophytic strains that occur in healthy leaves and lichen thalli in temperate and boreal North America. These endophytes frequently represent undescribed species. Here we examine two endophytic isolates of Coniochaeta from healthy photosynthetic tissue of Platycladus orientalis (Cupressaceae), a conifer cultivated for horticultural use in Arizona, USA. On the basis of morphology, in vitro assays, phylogenetic analyses of two loci, and analyses of whole genome data, we designate these endophytes as a novel species, Coniochaeta endophytica sp. nov. Strains of C. endophytica are closely related to an isolate from a native lichen in North Carolina, which we also characterize here. We compare C. endophytica with two known species that appear to be close relatives: C. prunicola, associated with wood necrosis in stonefruit trees in South Africa, and C. cephalothecoides, isolated from soil in Asia. The new species is distinct in phylogenetic, in vitro, and whole-genome analyses from C. prunicola, and differs slightly in conidiophore morphology from that species. Although available sequence data for C. cephalothecoides are of uncertain relation to the type specimen for that species, our results support the distinctiveness of C. endophytica on the basis of morphology, perithecial formation, and phylogenetic analyses. We discuss the challenge of identifying new species in the context of fungal ecology surveys, such as those for endophytes, which often rely only on a single locus and can misidentify taxa based on their closest matches in public databases or simple comparisons of barcode sequences alone.

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  • Abarenkov, K., Nilsson, R. H., Larsson, K. H., Alexander, I. J., Eberhardt, U., et al. 2010. The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytologist 186: 281–285.

  • Arnold, A. E. & Lutzoni, F. 2007. Diversity and host range of foliar endophytes: are tropical leaves biodiversity hotspots? Ecology 88: 541–549.

  • Asgari, B., Zare, R. & Gams, W. 2007. Coniochaeta ershadii, a new species from Iran, and a key to well-documented Coniochaeta species. Nova Hedwigia 84: 175–187.

  • Bills, G. F., González-Menéndez, V., Martín, J., Platas, G., Fournier, J., Persoh, D. & Stadler, M. 2012. Hypoxylon pulicicidum sp. nov. (Ascomycota, Xylariales), a pantropical insecticide-producing endophyte. PLoS One 7: e46687.

  • Broder, A. Z. 1998. On the resemblance and containment of documents. Compression and Complexity of Sequences. Proceedings 1998: 21–29.

  • Buchfink, B., Xie, C. & Huson, D. H. 2014. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12: 59–60.

  • Bussaban, B., Lumyong, S., Lumyong, P., Hyde, K. D. & McKenzie,

  • E. H. C. 2003. Three new species of Pyricularia are isolated as zingiberaceous endophytes from Thailand. Mycologia 95: 519–524.

  • Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., U´Ren, J. M., May, G. & Lutzoni, F. 2017. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics 33: 1160–1168.

  • Chen, K.-H., Miadlikowska, J., Molnár, K., Arnold, A. E., U´Ren, J. M., Gaya, E., Gueidan, C. & Lutzoni, F. 2015. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales and a new order – Phaeomoniellales. Molecular Phylogenetics and Evolution 85: 117–130.

  • Damm, U., Fourie, P. H. & Crous, P. W. 2010. Coniochaeta (Lecythophora), Collophora gen. nov. and Phaemoniella species associated with wood necroses of Prunus trees. Persoonia 24: 60–80.

  • Dayrat, B. 2005. Towards integrative taxonomy. Biological Journal of the Linnean Society 85: 407–415.

  • Del Olmo-Ruiz, M. 2012. Diversity, distributions, and host affiliations of fungal endophytes associated with seedless vascular plants (Ph.D dissertation). University of Arizona.

  • Dingua, L., Luo, R., Liu, C., Leung, C., Ting, H., Sadakane, K., Yamashita, H. & Lam, T. 2016. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102: 3–11.

  • Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792–1797.

  • Ewing, B., Hillier, L., Wendl, M. C. & Green, P. 1998. Base-calling of automated sequencer traces with phred. Genome Research 175–185.

  • Friebes, G., Jaklitsch, W. M., Garcia, S. & Voglmayr, H. 2016. Lopadostoma taeniosporum revisted and a new species of Coniochaeta. Sydowia 68: 87–97.

  • Gams, W. & McGinnis, M. R. 1983. Phialemonium, a new anamorph genus intermediate between Phialophora and Acremonium. Mycologia 75: 977–987.

  • García, D., Stchigel, A. M., Cano, J., Calduch, M., Hawksworth, D. L. & Guarro, J. 2006. Molecular phylogeny of Coniochaetales. Mycological Research 110: 1271–1289.

  • Gardes, M. & Bruns, T. D. 1993. ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113–118.

  • Gazis, R., Rehner, S. & Chaverri, P. 2011. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Molecular Ecology 20: 3001–3013.

  • Gazis, R., Miadlikowska, J., Lutzoni, F., Arnold, A. E. & Chaverri, P. 2012. Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes. Molecular Phylogenetics and Evolution 65: 294–304.

  • Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 15: 1072–1075.

  • Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., et al. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9: R7.

  • Han, J., Liu, C., L. Li, Zhou, H., Liu, L., Bao, L., Chen, Q., Song, F., Zhang, L., Li, E., Liu, L., et al. 2017. Decalin-containing tetramic acids and 4-Hydroxy-2-pyridones with antimicrobial and cytotoxic activity from the fungus Coniochaeta cephalothecoides collected in Tibetan Plateau (Medog). Journal of Organic Chemistry 82: 11474–11486.

  • Hibbett, D.S., Glotzer, D., Nilsson, R. H., Ohman, A., Nuhn, M. & Kirk, P. M. 2011. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biology Reviews 25: 38–47.

  • Hoffman, M. T. & Arnold, A. E. 2010. Diverse bacteria inhabit living hyphae of phylogenetically diverse fungal endophytes. Applied and Environmental Microbiology 76: 4063–4075.

  • Hoffman, M. T. & Arnold, A. E. 2008. Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees. Mycological Research 112: 331–344.

  • Huang, Y.-L., Devan, M. M. N., U´Ren, J. M., Furr, S. H. & Arnold, A. E. 2016. Pervasive effects of wildfire on foliar endophyte communities in montane forest trees. Microbial Ecology 71: 452–468.

  • Huhndorf, S. M., Miller, A. N. & Fernández, F. A. 2004. Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined. Mycologia 96: 368–387.

  • Ivanová, H. & Bernadovičová, S. 2012. New record of the fungus Coniochaeta prunicola on peaches from Slovakia. Biologia (Bratislava) 67: 269–273.

  • Kamiya, S., Uchiyama, S. & Udagawa, S. 1995. Two new species of Coniochaeta with a cephalothecoid peridium wall. Mycoscience 36: 377–383.

  • Katoh, K. & Standley, D. M. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements. Molecular Biology and Evolution 30: 772–780.

  • Khan, Z., Gene, J., Ahmad, S., Cano, J., Al-Sweih, N., Joseph, L., Chandy, R. & Guarro, J. 2013. Coniochaeta polymorpha, a new species from endotracheal aspirate of a preterm neonate, and transfer of Lecythophora species to Coniochaeta. Antonie Van Leeuwenhoek 104: 243–252.

  • Kirk, P., Cannon, P. F., Minter, D. W. & Stalpers, J. A. 2008. Ainsworth & Bisby’s Dictionary of the Fungi. 10th edn. CAB International, Wallingford, UK.

  • Kõljalg U., Nilsson, R. H., Abarenkov, K., Tedersoo, L., Taylor, A. F., Bahram, M., et al. 2013. Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology 22: 5271–5277.

  • Kornerup, A. & Wanscher, J. H. 1967. Methuen handbook of color. Methuen and Co., London.

  • Langmead, B. & Salzberg, S. L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357–359.

  • Lieckfeldt, E. & Seifert, K. A. 2000. An evaluation of the use of ITS sequences in the taxonomy of the Hypocreales. Studies in Mycology 45: 35–44.

  • Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y. O. & Borodovsky, M. 2005. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research 33: 6494–6506.

  • Lowe, T. M. & Eddy, S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955–964.

  • Maddison, W. P. & Maddison, D. R. 2017. Mesquite: a modular system for evolutionary analysis. Version 3.2.

  • Malloch, D. & Cain, R. F. 1971. New cleistothecial Sordariaceae and a new family, Coniochaetaceae. Canadian Journal of Botany 49: 869–880.

  • Martin, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal 17: 10–12.

  • Matheny, P. B., Yajuan, J. L., Ammirati, J. F. & Hall, B. D. 2002. Using RPB1 sequences to improve phylogenetic inferences among mushrooms (Inocybe, Agaricales). American Journal of Botany 89: 688–698.

  • Melin, E. & Nannfeldt, J.A. 1934. Researches into the blueing of ground woodpulp. Svenska Skogsvårdsföreningens Tidskrift 32: 397–616.

  • Nasr, S., Bien, S., Soudi, M. R., Alimadadi, N., Fazeli, S. A. S. & Damm, U. 2018. Novel Collophorina and Coniochaeta species from Euphorbia polycaulis, an edemic plant in Iran. Mycological Progress 17: 755–771.

  • Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., et al. 2016. Mash: fast genome and metagenome distance estimation with MinHash. Genome Biology 17: 132.

  • Palmer, J. M. 2016. Funannotate: a Fungal Genome Annotation and Comparative Genomics Pipeline. https://github.com/nextgenusfs/funannotate

  • Quaedvlieg, W., Binder, M., Groenewald, J. Z., Summerell, B. A., Carnegie, A. J., Burgess, T. I. & Crous, P. W. 2014. Introducing the consolidated species concept to resolve species in the Teratosphaeriaceae. Persoonia 33: 1–40.

  • Raja, H. A., Shearer, C. A., Fournier, J., & Miller, A. N. 2012. Freshwater ascomycetes: Coniochaeta gigantospora sp. nov. based on morphological and molecular data. Mycoscience 53: 373–380.

  • Réblová, M., Miller, A. N., Rossman, A. Y., Seifert, K. A., Crous, P. W., Hawksworth, D. L., et al. 2016. Recommendations for competing sexual-asexually typified generic names in Sordariomycetes (except Diaporthales, Hypocreales, and Magnaporthales). IMA Fungus 7: 131–153.

  • Rehner, S. A. & Buckley, E. 2005. A Beauveria phylogeny inferred from nuclear ITS and EF1-a sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97: 84–98.

  • Riddell, R. W. 1950. Permanent stained mycological preparations obtained by slide culture. Mycologia 42: 265–270.

  • Rojas, E. I., Herre, E. A., Mejía, L. C., Arnold, A. E., Chaverri, P. & Samuels, G. J. 2008. Endomelanconiopsis, a new anamorph genus in the Botryosphaeriaceae. Mycologia 100: 760–775.

  • Rojas, E. I., Rehner, S. A., Samuels, G. J., Van Bael, S. A., Herre, E. A., Cannon, P., Chen, R., et al. 2010. Colletotrichum gloeosporioides s. l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes. Mycologia 102: 1318–1338.

  • Rosling, A., Cox, F., Cruz-Martinez, K., Ihrmark, K., Grelet, G. A., Lindahl, B. D., Menkis, A. & James, T.Y. 2011. Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi. Science 333: 876–879.

  • Sahlin, K., Vezzi, F., Nystedt, B., Lundeberg, J. & Arvestad, L. 2014. BESST – Efficient scaffolding of large fragmented assemblies. BMC Bioinformatics 15: 281.

  • Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., et al. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109: 6241–6246.

  • Slater, G. S. & Birney, E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.

  • Smit, A. F. A., Hubley, R. & Green, P. 2013–2015. RepeatMasker Open-4.0. http://www.repeatmasker.org

  • Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S. & Morgenstern, B. 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleid Acids Research 34: W435-W439.

  • Stiller, J. W. & Hall, B. D. 1997. The origin of red algae: Implications for plastid evolution. Proceedings of the National Academy of Sciences of the United States of America 94: 4520–4525.

  • Torres-Cruz, T. J., Billingsley, T. T. L., Almatruk, M., Hesse, C. N., Kuske, C. R., Desiro, A., et al. 2017. Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats. Mycologia 109: 363–378.

  • U´Ren, J. M., Lutzoni, F., Miadlikowska, J, Laetsch, A. D. & Arnold, A. E. 2012. Host and geographic structure of endophytic and endolichenic fungi at a continental scale. American Journal of Botany 99: 898–914.

  • U´Ren, J. M., Miadlikowska, J., Zimmerman, N. B., Lutzoni, F., Stajich, J. E. & Arnold, A. E. 2016. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution 98: 210–232.

  • U´Ren, J. M. & Arnold, A. E. 2017. DNA extraction protocol for plant and lichen tissues stored in CTAB. Protocols.io, doi:10.17504/protocols.io.fs8bnhw

  • Valdecasas, A. G., Williams, D. M. & Wheeler, Q. D. 2007. “Integrative taxonomy” then and now: a response to Dayrat (2005). Biological Journal of the Linnean Society 93: 211–216.

  • Vázquez-Campos, X., Kinsela, A. S., White, T. D., Collins, R. N. & Neilan, B. A. 2014. Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov., two uranium mine-inhabiting Ascomycota fungi from northern Australia. Mycologia 106: 1073–1089.

  • Vilgalys, R. & Hester, M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238–4246

  • Weber, E. 2002. The Lecythophora­Coniochaeta complex I. Morphological studies on Lecythophora species isolated from Picea abies. Nova Hedwigia 74: 159–185.

  • Weber, E., Görke, C., & Begerow, D. 2002. The Lecythophora­Coniochaeta complex II. Molecular studies based on sequences of the large subunit of ribosomal DNA. Nova Hedwigia 74: 187–200.

  • Xie, J., Strobel, G. A., Feng, T., Ren, H., Mends, M. T., Zhou, Z. & Geary, B. 2015. An endophytic Coniochaeta velutina producing broad spectrum antimycotics. Journal of Microbiology 53: 390–397.

  • Zamora, J. C., & Calonge, F. D. 2015. Integrative taxonomy reveals an unexpected diversity in Geastrum section Geastrum (Geastrales, Basidiomycota). Persoonia 34: 130–165.

  • Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the Maximum Likelihood Criterion (PhD thesis). University of Texas at Austin.

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