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Aghdam SA, Lahowetz RM, Brown AMV. Divergent endophytic viromes and phage genome repertoires among banana ( Musa) species. Front Microbiol 2023; 14:1127606. [PMID: 37362937 PMCID: PMC10288200 DOI: 10.3389/fmicb.2023.1127606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Viruses generally cause disease, but some viruses may be beneficial as resident regulators of their hosts or host microbiomes. Plant-associated viruses can help plants survive by increasing stress tolerance or regulating endophytic communities. The goal of this study was to characterize endophytic virus communities in banana and plantain (Musa spp.) genotypes, including cultivated and wild species, to assess virome repertoires and detect novel viruses. Methods DNA viral communities were characterized by shotgun sequencing of an enriched endosphere extract from leaves and roots or corm of 7 distinct Musa genotypes (M. balbisiana, Thai Black, M. textilis, M. sikkimensis, Dwarf Cavendish, Williams Hybrid, and FHIA-25 Hybrid). Results Results showed abundant virus-like contigs up to 108,191 bp long with higher relative abundance in leaves than roots. Analyses predicted 733 phage species in 51 families, with little overlap in phage communities among plants. Phage diversity was higher in roots and in diploid wild hosts. Ackermanniviridae and Rhizobium phage were generally the most abundant taxa. A Rhizobium RR1-like phage related to a phage of an endophytic tumor-causing rhizobium was found, bearing a holin gene and a partial Shiga-like toxin gene, raising interest in its potential to regulate endophytic Rhizobiaceae. Klebsiella phages were of interest for possible protection against Fusarium wilt, and other phages were predicted with potential to regulate Erwinia, Pectobacterium, and Ralstonia-associated diseases. Although abundant phage-containing contigs were functionally annotated, revealing 1,038 predicted viral protein domains, gene repertoires showed high divergence from database sequences, suggesting novel phages in these banana cultivars. Plant DNA viruses included 56 species of Badnavirus and 26 additional non-Musa plant viruses with distributions that suggested a mixture of resident and transient plant DNA viruses in these samples. Discussion Together, the disparate viral communities in these plants from a shared environment suggest hosts drive the composition of these virus communities. This study forms a first step in understanding the endophytic virome in this globally important food crop, which is currently threatened by fungal, bacterial, and viral diseases.
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Abstract
RNA viruses usually have linear genomes and are encapsidated by their own capsids. Here, we newly identified four mycoviruses and two previously reported mycoviruses (a fungal reovirus and a botybirnavirus) in the hypovirulent strain SCH941 of Sclerotinia sclerotiorum. One of the newly discovered mycoviruses, Sclerotinia sclerotiorum yadokarivirus 1 (SsYkV1), with a nonsegmented positive-sense single-stranded RNA (+ssRNA) genome, was molecularly characterized. SsYkV1 is 5,256 nucleotides (nt) in length, excluding the poly(A) structure, and has a large open reading frame that putatively encodes a polyprotein with the RNA-dependent RNA polymerase (RdRp) domain and a 2A-like motif. SsYkV1 was phylogenetically positioned into the family Yadokariviridae and was most closely related to Rosellinia necatrix yadokarivirus 2 (RnYkV2), with 40.55% identity (78% coverage). Although SsYkV1 does not encode its own capsid protein, the RNA and RdRp of SsYkV1 are trans-encapsidated in virions of Sclerotinia sclerotiorum botybirnavirus 3 (SsBV3), a bisegmented double-stranded RNA (dsRNA) mycovirus within the genus Botybirnavirus. In this way, SsYkV1 likely replicates inside the heterocapsid comprised of the SsBV3 capsid protein, like a dsRNA virus. SsYkV1 has a limited impact on the biological features of S. sclerotiorum. This study represents an example of a yadokarivirus trans-encapsidated by an unrelated dsRNA virus, which greatly deepens our knowledge and understanding of the unique life cycles of RNA viruses. IMPORTANCE RNA viruses typically encase their linear genomes in their own capsids. However, a capsidless +ssRNA virus (RnYkV1) highjacks the capsid of a nonsegmented dsRNA virus for the trans-encapsidation of its own RNA and RdRp. RnYkV1 belongs to the family Yadokariviridae, which already contains more than a dozen mycoviruses. However, it is unknown whether other yadokariviruses except RnYkV1 are also hosted by a heterocapsid, although dsRNA viruses with capsid proteins were detected in fungi harboring yadokarivirus. It is noteworthy that almost all presumed partner dsRNA viruses of yadokariviruses belong to the order Ghabrivirales (most probably a totivirus or toti-like virus). Here, we found a capsidless +ssRNA mycovirus, SsYkV1, from hypovirulent strain SCH941 of S. sclerotiorum, and the RNA and RdRp of this mycovirus are trans-encapsidated in virions of a bisegmented dsRNA virus within the free-floating genus Botybirnavirus. Our results greatly expand our knowledge of the unique life cycles of RNA viruses.
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Mu F, Jia J, Xue Y, Jiang D, Fu Y, Cheng J, Lin Y, Xie J. Characterization of a novel botoulivirus isolated from the phytopathogenic fungus Sclerotinia sclerotiorum. Arch Virol 2021; 166:2859-2863. [PMID: 34291341 DOI: 10.1007/s00705-021-05168-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/22/2021] [Indexed: 10/20/2022]
Abstract
Sclerotinia sclerotiorum ourmiavirus 17 (SsOV17) was isolated from the hypovirulent strain GF3 of Sclerotinia sclerotiorum. The genome of SsOV17 is 2,802 nt in length and contains a single long open reading frame (ORF) flanked by a short structured 5'-untranslated region (5'-UTR) (28 nt) and a long 3'-UTR (788 nt), respectively. The ORF encodes a protein with 663 amino acids and a predicted molecular mass of 75.0 kDa. A BLASTp search indicated that the protein encoded by SsOV17 is closely related to the putative RNA-dependent RNA polymerase (RdRp) of Sclerotinia sclerotiorum ourmiavirus 13 (71% identity). A multiple sequence alignment indicated that eight conserved amino acid motifs were present in the RdRp conserved region of SsOV17. Phylogenetic analysis demonstrated that SsOV17 clustered with members of the genus Botoulivirus.
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Affiliation(s)
- Fan Mu
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunxiang Xue
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanping Fu
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang Lin
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Qu Z, Fu Y, Lin Y, Zhao Z, Zhang X, Cheng J, Xie J, Chen T, Li B, Jiang D. Transcriptional Responses of Sclerotinia sclerotiorum to the Infection by SsHADV-1. J Fungi (Basel) 2021; 7:493. [PMID: 34206246 PMCID: PMC8303302 DOI: 10.3390/jof7070493] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
The infection by a single-stranded DNA virus, Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), causes hypovirulence, a reduced growth rate, and other colony morphological changes in its host Sclerotinia sclerotiorum strain DT-8. However, the mechanisms of the decline are still unclear. Using digital RNA sequencing, a transcriptome analysis was conducted to elucidate the phenotype-related genes with expression changes in response to SsHADV-1 infection. A total of 3110 S. sclerotiorum differentially expressed genes (DEGs) were detected during SsHADV-1 infection, 1741 of which were up-regulated, and 1369 were down-regulated. The identified DEGs were involved in several important pathways. DNA replication, DNA damage response, carbohydrate and lipid metabolism, ribosomal assembly, and translation were the affected categories in S. sclerotiorum upon SsHADV-1 infection. Moreover, the infection of SsHADV-1 also suppressed the expression of antiviral RNA silencing and virulence factor genes. These results provide further detailed insights into the effects of SsHADV-1 infection on the whole genome transcription in S. sclerotiorum.
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Affiliation(s)
- Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Zhenzhen Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Xuekun Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Q.); (Z.Z.); (X.Z.); (J.C.); (J.X.); (T.C.); (B.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Aghdam SA, Brown AMV. Deep learning approaches for natural product discovery from plant endophytic microbiomes. ENVIRONMENTAL MICROBIOME 2021; 16:6. [PMID: 33758794 PMCID: PMC7972023 DOI: 10.1186/s40793-021-00375-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 05/10/2023]
Abstract
Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich 'in planta' community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s40793-021-00375-0.
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Affiliation(s)
- Shiva Abdollahi Aghdam
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
| | - Amanda May Vivian Brown
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX 79409 USA
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