Please wait a minute...
Journal of Integrative Agriculture  2020, Vol. 19 Issue (9): 2257-2264    DOI: 10.1016/S2095-3119(20)63164-1
Special Issue: 植物抗病遗传合辑Plant Disease-resistance Genetics 植物细菌真菌合辑Plant Bacteria/Fungus
Plant Protection Advanced Online Publication | Current Issue | Archive | Adv Search |
Diversity in metagenomic sequences reveals new pathogenic fungus associated with smut in Job’s tears
LI Xiang-dong1, 2, SHI Ming1, PAN Hong1, 2, LU Xiu-juan1, 2, WEI Xin-yuan1, 2, LU Ping3, LIAN Qi-xian4, FU Yu-hua5 
1 Southwest Guizhou Institute of Karst Regional Development, Xingyi 562400, P.R.China
2 Adlay of Engineering Technical Research Centre in Guizhou, Xingyi 562400, P.R.China
3 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
4 Xingyi Normal University for Nationalities, Xingyi 562400, P.R.China
5 Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi 562400, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract  
Smut is a serious disease in Job’s tears, also known as adlay, and contributes to the reduction of crop yield in agricultural fields.  In this study, the key pathogenic fungi in adlay smut disease were first identified by internal transcribed spacer region (ITS) high-throughput sequencing and then used to elucidate the composition and diversity of the fungal community in adlay smut.  Results indicate that an abundance of operational taxonomic units (OTUs) were detected in the infected involucres of flowering plants and the OTUs were classified to nine phyla, 20 classes, 45 orders, 90 families and 119 genera.  A total of 4 986 OTUs clustered together, sharing six core OTUs in all samples, while 145 OTUs were shared among four geographical groups.  The Shannon and Simpson indices ranged from 0.137–1.629 and 0.357–0.970, respectively.  Community diversity ranked as Anshun (AS)>Qinglong (QL)>Xingren (XR)>Xingyi (XY) among the four geographical groups by Shannon and Simpson indices, exhibiting complex community diversities among accessions and geographical groups.  The richness and diversity data imply a weak relationship between the accession community richness and geographical origins of samples.  Two closely related fungal genera, Sporisorium and Ustilago, were implicated as causes of smut disease.  The genus Sporisorium appears to be more commonly found among accessions and thus is more likely to be the fungal pathogen causing smut in adlay.  This work can facilitate strategies to control and prevent smut infection to improve adlay yield.
Keywords:  metagenomic        ITS        smut        Job’s tears  
Received: 30 September 2019   Accepted:
Fund: This work was financially supported by the Science and Technology Program in Guizhou Province, China (20162608, 20162569), the High-Level Innovative Talents Training Project in Guizhou Province, China (20154016), and the Southwest Guizhou of Science and Technology Program, China (2017-1-2).
Corresponding Authors:  Correspondence LI Xiang-dong, Mobile: +86-15186451604, E-mail: lixiangdongsiji@163.com; SHI Ming, Mobile: +86-18685951616, E-mail: shiming1616@126.com   

Cite this article: 

LI Xiang-dong, SHI Ming, PAN Hong, LU Xiu-juan, WEI Xin-yuan, LU Ping, LIAN Qi-xian, FU Yu-hua. 2020. Diversity in metagenomic sequences reveals new pathogenic fungus associated with smut in Job’s tears. Journal of Integrative Agriculture, 19(9): 2257-2264.

Barnabas L, Ashwin N M R, Ramesh Sundar A, Malathi P, Viswanathan R. 2017. Putative orthologs of Ustilago maydis effectors screened from the genome of sugarcane smut fungus - Sporisorium scitamineum. Australasian Plant Pathology, 2, 147–156.
Chao A. 1984. Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11, 265–270.
Chen M C, Zhu Y J, Liu B, Wang J P, Liu X G, Yang W J. 2018. Diversity research of the soil bacteria of Jasminum sambac Ait based on metagenome. Journal of Agricultural Biotechnology, 9, 1480–1493. (in Chinese)
Chen Q Q, Liu B, Guan X, Tang J Y. 2014. Analysis of Anoectochilus roxburghii root microbial diversity by metagenomic technology. Journal of Agricultural Biotechnology, 11, 1441–1446. (in Chinese)
Chowdhury S. 1946. Some studies on the smut Ustilago coicis Bref. of Job’s tears millet. Journal of Indian Botany Social, 25, 123–130.
Cooke D E L, Drenth A, Duncan J M, Wagels G, Brasier C M. 2000. A molecular phylogeny of Phytophthora and related oomycetos. Fungal Genetics and Biology, 30, 17–32.
Deng Y Z, Zhang B, Chang C Q, Wang Y X, Lu S, Sun S Q, Zhang X M, Chen B S, Jiang Z D. 2018. The MAP kinase SsKpp2 is required for mating/filamentation in Sporisorium scitamineum. Frontiers in Microbiology, 9, 2555.
Edgar R C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 19, 2460–2461.
Ghareeb H, Zhao Y, Schirawski J. 2019. Sporisorium reilianum possesses a pool of effector proteins that modulate virulence on maize. Molecular Plant Pathology, 1, 124–136.
Hang B, Cui G B, Chang C Q, Wang Y X, Zhang H Y, Chen B S, Deng Y Z, Jiang Z D. 2019. The autophagy gene ATG8 affects morphogenesis and oxidative stress tolerance in Sporisorium scitamineum. Journal of Integrative Agriculture, 5, 1024–1034.
Hou J N, Li W, Yang X J, Sun Y, Xie D Y, Wang M M, Fang W P, Zhao F A. 2019. Transformation of green fluorescent protein in Fusarium oxysporum of cotton. Molecular Plant Breeding, 10, 3247–3252. (in Chinese)
Hu S P, Yu J, Wei K F, Lan B, Li M Q, Xie B Y, Zhu Y C, Yang Y N, Zhu J M, Zhang L, Li X M. 2019. Studies on the biological characteristics and pathogenic identification of rice spikelet rot disease in Jiangxi province. Acta Agriculturae Universitatis Jiangxiensis, 2, 234–242. (in Chinese)
Huson D H, Mitra S, Ruscheweyh H J, Weber N, Schuster S C. 2011. Integrative analysis of environmental sequences using MEGAN4. Genome Research, 9, 1552–1560.
Levy L, Castlebury L A, Carris L M, Meyer R J, Pimentel G. 2001. Internal transcribed spacer sequence-based phylogeny and polymerase chain reaction restriction fragment length polymorphism differentiation of Tilletia walkeri and T. indica. Phytopathology, 91, 935–940.
Mundkur B B. 1940. A second contribution towards a knowledge of Indian Ustilaginales: Fragments xxvi-l. Transactions of the British Mycological Society, 3–4, 312–336.
Normile D, Yimin D. 2003. The new face of traditional Chinese medicine. Science, 299, 188–190.
Piepenbring M, Bauer R, Oberwinkler F. 1998. Teliospores of smut fungi-general aspects of teliospore walls and sporogenesis. Protoplasma, 204, 155–169.
Ruan W J, Lai M D, Zhou J G. 2006. Anticancer effects of Chinese herbal medicine, science or myth? Journal of Zhejiang University (Science B: Biomedicine & Biotechnology), 7, 1006–1014.
Schloss P D, Westcott S L, Ryabin T. 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 23, 7537–7541.
Small W. 1927. Matter of phytopathological interest during 1926. Review of Applied Mycological, 6, 273–274.
Stoll M, Begerow D, Oberwinkler F. 2005. Molecular phylogeny of Ustilago, Sporisorium, and related taxa based on combined analyses of rDNA sequences. Mycological Research, 3, 342–356.
Stoll M, Piepenbring M, Begerow D, Oberwinkler F. 2003. Molecular phylogeny of Ustilago and Sporisorium species (Basidiomycota, Ustilaginales) based on internal transcribed spacer (ITS) sequences. Canadian Journal of Botany, 9, 976–984.
Su J K, Xu D, Guo L, Luo J M, Shao D Y, Yun F, Cai J B. 2017. Diversity analysis of microorganism on flue-cured tobacco leaf surface based on metagenome sequencing. Genomics and Applied Biology, 4, 1538–1545. (in Chinese)
Vánky K. 1998. A survey of the spore-ball-forming smut fungi. Mycological Research, 5, 513–526.
Wang Q, Garrity G M, Tiedje J M, Cole J R. 2007. Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 16, 5261–5267.
Zhang J Z, Peigang G, Gang T. Mohammad R O, Kevin D H. 2013. Ultrastructure and phylogeny of Ustilago coicis. Journal of Zhejiang University (Science B: Biomedicine & Biotechnology), 4, 336–345.
Zhao Q, Deng Y Y, Li W, Sun H Y, Xia Y L, Chen H G. 2017. Analysis of endophytes diversity in wheat seedlings by metagenomic technology. Acta Phytopathologica Sinica, 3, 313–324. (in Chinese)
Zhao Z X, Ling B, Yan W R, Zeng X P, Xiao M, Chen Y. 2019. Isolation, identification and phylogenetic analysis of pepper wilt. Molecular Plant Breeding, 19, 6383–6389. (in Chinese)
Zhou Y, Chao G M, Liu J J, Zhu M Q, Wang Y, Feng B L. 2016. Genetic diversity of Ustilago hordei in Tibetan areas as revealed by RAPD and SSR. Journal of Integrative Agriculture, 10, 2299–2308.
[1] NI Chun-hui, HAN Bian, LIU Yong-gang, Maria MUNAWAR, LIU Shi-ming, LI Wen-hao, SHI Ming-ming, LI Hui-xia, PENG De-liang.

Diagnosis and characterization of the ribosomal DNA-ITS of potato rot nematode (Ditylenchus destructor) populations from Chinese medicinal herbs [J]. >Journal of Integrative Agriculture, 2023, 22(6): 1763-1781.

[2] ZHAO Ruo-nan, CHEN Si-yuan, TONG Cui-hong, HAO Jie, LI Pei-si, XIE Long-fei, XIAO Dan-yu, ZENG Zhen-ling, XIONG Wen-guang. Insights into the effects of pulsed antimicrobials on the chicken resistome and microbiota from fecal metagenomes[J]. >Journal of Integrative Agriculture, 2023, 22(6): 1857-1869.
[3] CUI Jiang-kuan, PENG Huan, LIU Shi-ming, Gul Erginbas Orakci, HUANG Wen-kun, Mustafa Imren, Abdelfattah Amer Dababat, PENG De-liang . Occurrence, identification and phylogenetic analyses of cereal cyst nematodes (Heterodera spp.) in Turkey[J]. >Journal of Integrative Agriculture, 2017, 16(08): 1767-1776.
No Suggested Reading articles found!