Dataset Information

Molecular characterization of leaf spot fungi using internal transcribed spacer (ITS) based phylogenetic inference.

ABSTRACT: The plant pathogenic leaf spot fungi cause loss in crop yield. Fungi and other pathogens such as a virus, bacteria, cause leaf spot diseases and nematodes play a secondary role. Therefore, it is of interest to study internal transcribed spacer (ITS) sequence from the plant pathogenic fungi. Hence, we collected nineteen different isolates at Madurai Kamaraj University, Tamilnadu, India for this study. We report nineteen positive isolates identified with species-level characterization using ITS sequence supported with a phylogenetic tree and corresponding secondary structure analysis.

SUBMITTER: Chitrakani B

PROVIDER: S-EPMC6651034 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Molecular characterization of leaf spot fungi using internal transcribed spacer (ITS) based phylogenetic inference.

Chitrakani Bose B Sureshkumar Senthuran S Rajapriya Pandy P Pandi Mohan M

Bioinformation 20190203 1

The plant pathogenic leaf spot fungi cause loss in crop yield. Fungi and other pathogens such as a virus, bacteria, cause leaf spot diseases and nematodes play a secondary role. Therefore, it is of interest to study internal transcribed spacer (ITS) sequence from the plant pathogenic fungi. Hence, we collected nineteen different isolates at Madurai Kamaraj University, Tamilnadu, India for this study. We report nineteen positive isolates identified with species-level characterization using ITS se ...[more]

PMID: 31359999

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Project description:Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.

Dataset Information

Molecular characterization of leaf spot fungi using internal transcribed spacer (ITS) based phylogenetic inference.

Publications

Molecular characterization of leaf spot fungi using internal transcribed spacer (ITS) based phylogenetic inference.

Similar Datasets

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