title: Endophytic Diaporthe from Southeast China are genetically diverse based on multi-locus phylogeny analyses.
abstract: Species of Diaporthe (anamorph Phomopsis) comprise a diverse and widely distributed group of phytopathogens, saprophytes and endophytes. However, the degree of genetic diversity of endophytic Diaporthe has not yet been fully investigated. In this paper, a survey of endophytes from 28 plants in southeast China yielded 116 Diaporthe isolates, out of which 64 haplotypes were determined using DnaSP ver. 5.1 based on alignment result of internal transcribed spacer of ribosomal nucleotide sequences (ITS rDNA). Many haplotypes turned out to be quite different from known species and displayed high diversity. Among them, 14 strains from 5 discriminating terminal clades were selected to go through further analysis according to partial sequence of translation elongation factor 1-α (tef1-α) and again they got separated from others. The following multi-gene phylogenetic analysis based on ITS rDNA, tef1-α, β tubulin and calmodulin grouped eight most discrepant strains into three distinctive clusters, cluster 1 (Rc001, Eu004 and Eu009), cluster 2 (ZJWCF252, Sjm001 and Ac001) and cluster 3 (Pcs013 and Sfp005) respectively with high support values. These clusters above represent three potentially novel species. This research provides strong evidence of high biodiversity and novelty of Diaporthe endophytes from southeast China, which is thus important not only for better resolving the taxonomy in this genus, but also for further utilization due to their multiple application.
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Jiaying
authors.initials: J
authors.lastname: Wang
authors.forename: Xihui
authors.initials: X
authors.lastname: Xu
authors.forename: Lijuan
authors.initials: L
authors.lastname: Mao
authors.forename: Jiaping
authors.initials: J
authors.lastname: Lao
authors.forename: Fucheng
authors.initials: F
authors.lastname: Lin
authors.forename: Zhilin
authors.initials: Z
authors.lastname: Yuan
authors.forename: Chulong
authors.initials: C
authors.lastname: Zhang
mesh_terms: D001203:Ascomycota / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D002147:Calmodulin / Q000235:genetics; D002681:China; D016000:Cluster Analysis; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D014644:Genetic Variation; D020648:Peptide Elongation Factor 1 / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000382:microbiology; D017422:Sequence Analysis, DNA; D014404:Tubulin / Q000235:genetics
chemical_list: D002147:Calmodulin; D021903:DNA, Ribosomal Spacer; D020648:Peptide Elongation Factor 1; D014404:Tubulin
references.citation: FEMS Microbiol Lett. 2007 May;270(1):90-6
references.pmid: 17302921
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: PLoS One. 2012;7(10):e46687
references.pmid: 23056404
references.citation: Persoonia. 2013 Dec;31:1-41
references.pmid: 24761033
references.citation: New Phytol. 2009;182(2):314-330
references.pmid: 19236579
references.citation: Fungal Biol. 2010 Feb-Mar;114(2-3):255-70
references.pmid: 20943136
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Int J Mol Sci. 2012 Nov 30;13(12):16255-66
references.pmid: 23203194
references.citation: Front Biosci (Elite Ed). 2012 Jan 01;4:2045-70
references.pmid: 22202019
references.citation: FEMS Microbiol Lett. 2010 Jun;307(1):94-101
references.pmid: 20402786
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: Fungal Biol. 2010 Oct;114(10):797-808
references.pmid: 20943189
references.citation: J Microbiol. 2011 Feb;49(1):15-23
references.pmid: 21369974
references.citation: Mycologia. 1972 Mar-Apr;64(2):316-24
references.pmid: 5063030
references.citation: Appl Microbiol Biotechnol. 2012 Jul;95(1):47-59
references.pmid: 22622838
references.citation: Stud Mycol. 2006;55:65-74
references.pmid: 18490972
references.citation: Appl Microbiol Biotechnol. 2011 Jun;90(6):1829-45
references.pmid: 21523479
references.citation: Clin Microbiol Infect. 2011 Oct;17(10):1492-4
references.pmid: 21781209
references.citation: Fungal Biol. 2011 Mar;115(3):197-213
references.pmid: 21354526
references.citation: Braz J Microbiol. 2012 Jul;43(3):1174-82
references.pmid: 24031942
references.citation: Int J Biol Sci. 2005;1(1):24-33
references.pmid: 15951847