Secondary structure of nrDNA Internal Transcribed Spacers as a useful tool to align highly divergent species in phylogenetic studies

Giudicelli, Giovanna Câmara; Mäder, Geraldo; Silva‐Arias, Gustavo A.; Zamberlan, Priscilla Mena; Bonatto, Sandro L.; Freitas, Loreta B.

doi:10.1590/1678-4685-gmb-2016-0042

Cited by 8 publications

(5 citation statements)

References 64 publications

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“…Lately, the significance of this phenomenon in plant speciation and evolution has been well defended [ 34 , 35 ]. The usage of nrDNA (especially ITS region) to detect hybrids has been widely implemented in plant studies due to its remarkable proprieties; we mention the homogenous paralogs within individuals as a result of concerted evolution [ 36 , 37 ]. As well, this marker was highly explored in nearly all Juniperus taxa (including haplotypes within taxa) for phylogenetic purposes and showed high efficiency in junipers hybridization studies with relatively good number of informative SNPs [ 5 , 6 , 8 , 10 , 11 , 15 , 17 , 21 , 29 ].…”

Section: Discussionmentioning

confidence: 99%

Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations

et al. 2020

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Background Gene flow and polyploidy have been found to be important in Juniperus evolution. However, little evidence has been published elucidating the association of both phenomena in juniper taxa in the wild. Two main areas were studied in Spain (Eastern Iberian Range and Sierra de Baza) with both diploid and tetraploid taxa present in sympatry. Gene flow and ploidy level were assessed for these taxa and the resulted offspring. Results Twenty-two allo-triploid hybrids between J. sabina var. sabina and J. thurifera were found in the Eastern Iberian Range population. However, in the Sierra de Baza population no triploids were found. Instead, 18 allo-tetraploid hybrids between two tetraploid taxa: J. sabina var. balkanensis and J. thurifera were discovered. High genetic diversity was exhibited among the tetraploid hybrids at Sierra de Baza, in contrast to the genetically identical triploid hybrids at the Eastern Iberian Range; this suggests meiotic difficulties within the triploid hybrids. In addition, unidirectional gene flow was observed in both studied areas. Conclusion Polyploidy and hybridization can be complementary partners in the evolution of Juniperus taxa in sympatric occurrences. Juniperus was shown to be an ideal coniferous model to study these two phenomena, independently or in concert.

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Section: Discussionmentioning

confidence: 99%

Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations

et al. 2020

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“…2012 ), as was the case in an unnamed Alaskan soil fungus ( Glass et al 2014 ). Other tools to be tested to potentially detect aberrant and artifactual sequences include assessing the secondary structure of ITS reads ( Goertzen et al 2003 , Morrison 2009 , Glass et al 2013 , Koetschan et al 2014 , Coleman 2015 , Giudicelli et al 2017 ). The likelihood of artifactual sequences obtained from different studies being so similar that they form a well-defined and well-supported species-level clade is remote.…”

Section: Potential Pitfalls Of Dna Sequence Typesmentioning

confidence: 99%

Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

Lücking

Hawksworth

2018

IMA Fungus

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There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample (‘bag’ type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code.Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence...

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“…For instance, the phylogeny of the species from the genus Ampelomyces are primarily based on the ITS region, where some contrasting results have been obtained. Interesting, the utility of Ampelomyces ITS2 secondary structures (S2s) to study its phylogeny has not been investigated even when several works have demonstrated ITS2 S2s can provide with important features to improve phylogenetic analyses [13,15]. Ampelomyces spp.…”

Section: Introductionmentioning

confidence: 99%

“…In order to resolve these issues and contribute to knowledge and future research in this area, we have investigated whether ITS2 S2s contain specific features that may be incorporated into phylogenetic analysis and provide with novel important information regarding evolutive processes occurring in Ampelomyces . Indeed, the utility of the ITS2 S2 to study the phylogeny of several organisms have been demonstrated [ 15 , 35 ] but it has not been investigated in Ampelomyces .…”

Section: Introductionmentioning

confidence: 99%

The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

2021

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Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.

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Secondary structure of nrDNA Internal Transcribed Spacers as a useful tool to align highly divergent species in phylogenetic studies

Cited by 8 publications

References 64 publications

Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations

Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations

Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

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