Multiple Group I Introns in the Small-Subunit rDNA of Botryosphaeria dothidea: Implication for Intraspecific Genetic Diversity

Xu, Chao; Wang, Chunsheng; Sun, Xin-Yao; Zhang, Rong; Tanaka, Eiji; Sun, Guangyu

doi:10.1371/journal.pone.0067808

Cited by 9 publications

(8 citation statements)

References 40 publications

(48 reference statements)

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“…Preliminary secondary structural models of the sequences inserted in the SSU rDNA of IFM 53848 T were predicted by using the UNAFold Web Server [http://unafold.rna. albany.edu/; Zuker, 2003) and then manually modified and optimized by referring to previous studies of group I introns (Burke et al, 1987;Cech et al, 1994;Machouart-Dubach et al, 2002;Machouart et al, 2004;Xu et al, 2013).…”

Section: Methodsmentioning

confidence: 99%

Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis

Masuda

Hirose

Ishikawa

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Species of the genus Prototheca are achlorophyllous algae and ubiquitous in nature, and so far, six species have been listed in this genus: Prototheca wickerhamii, Prototheca zopfii, Prototheca blaschkeae, Prototheca cutis, Prototheca stagnora and Prototheca ulmea. A strain of the genus Prototheca, IFM 53848 T , was isolated in Japan from a patient with systemic protothecosis and had been designated P. wickerhamii. Our previous study, by using PCR analysis, revealed that its SSU rRNA gene (rDNA) was distinctively larger than that of P. wickerhamii and other species of the genus Prototheca. In this study, molecular analysis showed that the exceptionally large SSU rDNA of IFM 53848 T contains four group I introns. The morphology of IFM 53848 T was indistinguishable from those of P. wickerhamii or P. cutis, and phylogenetic analyses, based on the sequences of the SSU rDNA exons and the D1/D2 region of the large subunit rDNA, indicated that IFM 53848 T was closely related to P. cutis. On the other hand, unlike P. cutis, IFM 53848 T failed to assimilate fructose or lysine and grew well at higher temperatures of up to 42 8C. In addition, the nucleotide sequence of the ribosomal internal transcribed spacer and the matrix assisted laser desorption ionization time-of-flight mass spectrometry profile of IFM 53848 T were clearly distinct from those of P. cutis. The results strongly suggest that IFM 53848 T represents a novel species, and so the seventh member of the genus Prototheca, which we have named Prototheca miyajii sp. nov. The unique characteristics of the strain may provide useful insights into the systematic taxonomy of the genus Prototheca.

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Section: Methodsmentioning

confidence: 99%

Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis

Masuda

Hirose

Ishikawa

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…Group I introns are widespread and have been reported from nuclear rDNA (18S and 26S RNA genes) in fungi, protozoans, metazoans [36][37][38][39][40][49][50][51][52][53][54][55][56][57][58], bacterial genomes, phages and viruses, archaeal genomes, and they are encountered frequently in mitochondrial and plastid genomes (reviewed in [59]). With regard to metazoans, Group I introns have been noted in the mitochondrial genomes in members of Placozoa, Anthozoa, and Porifera [54,56,57].…”

Section: Distribution and Impact Of Introns On Organellar Genome Architecturementioning

confidence: 99%

Organellar Introns in Fungi, Algae, and Plants

Mukhopadhyay

Hausner

2021

Cells

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Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

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“…This cryptic species demonstrated substantial genetic and biological distinctions from B. dothidea . For example, the two species possessed different number and length of group I introns in the primary structures of the 18S rDNA (Xu et al . 2013, 2015).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation

2018

Self Cite

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Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and B. kuwatsukai. Here, we sequenced the genomes of B. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and B. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat rate), and conducted a comparative analysis of these two genomes, as well as other sequenced fungal genomes, in order to understand speciation and distinctive patterns of evolution of pathogenicity-related genes. Pair-wise genome alignments revealed that the two species are highly syntenic (96.74 % average sequence identity). Both species encode a significant number of pathogenicity-related genes, e.g. carbohydrate active enzymes (CAZYs), plant cell wall degrading enzymes (PCWDEs), secondary metabolites (SMs) biosynthetic enzymes, cytochrome P450 enzymes (CYPs), and secreted peptidases, in comparison to all additional sequenced fungal species involved in various life-styles. The number of pathogenicity-related genes in B. dothidea and B. kuwatsukai is higher than other genomes of Botryosphaeriaceae pathogens (Macrophomina phaseolina and Neofusicoccum parvum), suggesting a secondary round of Botryosphaeria-lineage expansion in the family. There were, however, also significant differences in the genomes of the two Botryosphaeria species. Botryosphaeria kuwatsukai, which infects only apple and pear, apparently lost a set of SMs genes, CAZYs and PCWDEs, possibly as a result of host specialization. Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. Our results will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security.

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Multiple Group I Introns in the Small-Subunit rDNA of Botryosphaeria dothidea: Implication for Intraspecific Genetic Diversity

Cited by 9 publications

References 40 publications

Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis

Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis

Organellar Introns in Fungi, Algae, and Plants

Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation

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