Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea)

Alvizu, Adriana; Eilertsen, Mari Heggernes; Xavier, Joana R.; Rapp, Hans Tore

doi:10.1007/s13127-018-0368-4

Cited by 21 publications

(11 citation statements)

References 53 publications

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“…Hence, the information that is provided is insufficient to fully resolve the phylogeny of minor classes. As more T9SS-acquiring species from minor classes are sequenced later on, the phylogeny of T9SS protein components will be more resolved (Alvizu et al, 2018). Different from the other 19 BI trees of T9SS protein components, the BI tree of PorR does not exhibit monophyletic clades for all major classes under Bacteroidetes (Figs.…”

Section: Discussionmentioning

confidence: 93%

Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer

Emrizal

Muhammad

2020

PeerJ

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Porphyromonas gingivalis is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that ultimately leads to tooth loss. Virulence factors that contribute to periodontitis are secreted by Type IX Secretion System (T9SS). There are aspects of T9SS protein components that have yet to be characterised. Thus, the aim of this study is to investigate the phylogenetic relationship between members of 20 T9SS component protein families. The Bayesian Inference (BI) trees for 19 T9SS protein components exhibit monophyletic clades for all major classes under Bacteroidetes with strong support for the monophyletic clades or its subclades that is consistent with phylogeny exhibited by the constructed BI tree of 16S rRNA. The BI tree of PorR is different from the 19 BI trees of T9SS protein components as it does not exhibit monophyletic clades for all major classes under Bacteroidetes. There is strong support for the phylogeny exhibited by the BI tree of PorR which deviates from the phylogeny based on 16S rRNA. Hence, it is possible that the porR gene is subjected to horizontal transfer as it is known that virulence factor genes could be horizontally transferred. Seven genes (porR included) that are involved in the biosynthesis of A-LPS are found to be flanked by insertion sequences (IS5 family transposons). Therefore, the intervening DNA segment that contains the porR gene might be transposed and subjected to conjugative transfer. Thus, the seven genes can be co-transferred via horizontal gene transfer. The BI tree of UgdA does not exhibit monophyletic clades for all major classes under Bacteroidetes which is similar to the BI tree of PorR (both are a part of the seven genes). Both BI trees also exhibit similar topology as the four identified clusters with strong support and have similar relative positions to each other in both BI trees. This reinforces the possibility that porR and the other six genes might be horizontally transferred. Other than the BI tree of PorR, the 19 other BI trees of T9SS protein components also exhibit evidence of horizontal gene transfer. However, their genes might undergo horizontal gene transfer less frequently compared to porR because the intervening DNA segment that contains porR is easily exchanged between bacteria under Bacteroidetes due to the presence of insertion sequences (IS5 family transposons) that flank it. In conclusion, this study can provide a better understanding about the phylogeny of T9SS protein components.

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Section: Discussionmentioning

confidence: 93%

Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer

Emrizal

Muhammad

2020

PeerJ

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“…In total, the dataset includes 144 different morphospecies, and a total of 807 specimens. Several studies were based on this dataset: Alvizu et al (in press); Bertolino et al 2009; Calcinai et al 2000; Cattaneo-Vietti et al 2000; Fondi et al 2014; Mangano et al 2009; Orlandini et al 2014; Papaleo et al 2012, 2013; Romoli et al 2011; Sarà 2002; Sarà et al 1992. The validity and synonyms of each species name were checked in WORMS (World Register of Marine Species; http://www.marinespecies.org; last check made on 2018-03-28).…”

Section: Taxonomic Coveragementioning

confidence: 99%

Porifera collection of the Italian National Antarctic Museum (MNA), with an updated checklist from Terra Nova Bay (Ross Sea)

Ghiglione¹,

Alvaro²,

Cecchetto³

et al. 2018

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This new dataset presents occurrence data for Porifera collected in the Ross Sea, mainly in the Terra Nova Bay area, and curated at the Italian National Antarctic Museum (MNA, section of Genoa). Specimens were collected in 331 different sampling stations at depths ranging from 17 to 1,100 meters in the framework of 17 different Italian Antarctic expeditions funded by the Italian National Antarctic Research Program (PNRA). A total of 807 specimens, belonging to 144 morphospecies (i.e., 95 taxa identified at species level and 49 classified at least at the genus level) is included in the dataset. Nearly half (45%) of the species reported here correspond to species already known for Terra Nova Bay. Out of the remaining 55% previously unknown records, under a third (~29%) were classified at the species level, while over a quarter (~26%) were ascribed to the genus level only and these would require further study. All vouchers are permanently curated at the MNA and are available for study to the scientific community. A 3D model of an uncommon species from the Ross Sea, i.e. Tethyopsisbrondstedi (Burton, 1929), is also presented and will be made available for outreach purposes.

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“…Sponges are admittedly a challenging group to work with in taxonomy. Thanks to an increasing amount of molecular data, the traditional classifications have seen some drastic changes these last years, in the four classes of sponges: Demospongiae [ 88 , 89 ], Hexactinellida [ 90 ], Calcarea [ 91 , 92 ] and Homoscleromorpha [ 93 ]. These changes, added to the subtleties and caveats of spicule terminology, the dense taxonomy literature (not free of identification errors) make sponge taxonomy a challenging field for a non-specialist.…”

Section: Discussionmentioning

confidence: 99%

Good Practices in Sponge Natural Product Studies: Revising Vouchers with Isomalabaricane Triterpenes

et al. 2022

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Species misidentification in the field of natural products is an acknowledged problem. These errors are especially widespread in sponge studies, albeit rarely assessed and documented. As a case study, we aim to revisit reports of isomalabaricane triterpenes, isolated from four demosponge genera: Jaspis, Geodia, Stelletta and Rhabdastrella. From a total of 44 articles (1981–2022), 27 unique vouchers were listed, 21 of which were accessed and re-examined here: 11 (52.4%) of these were misidentified. Overall, 65.9% of the studies published an incorrect species name: previously identified Jaspis and Stelletta species were all in fact Rhabdastrella globostellata. We conclude that isomalabaricane triterpenes were isolated from only two Rhabdastrella species and possibly one Geodia species. In addition to shedding a new light on the distribution of isomalabaricane triterpenes, this study is an opportunity to highlight the crucial importance of vouchers in natural product studies. Doing so, we discuss the impact of species misidentification and poor accessibility of vouchers in the field of sponge natural products. We advocate for stricter voucher guidelines in natural product journals and propose a common protocol of good practice, in the hope of reducing misidentifications in sponge studies, ensure reproducibility of studies, and facilitate follow-up work on the original material.

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Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea)

Cited by 21 publications

References 53 publications

Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer

Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer

Porifera collection of the Italian National Antarctic Museum (MNA), with an updated checklist from Terra Nova Bay (Ross Sea)

Good Practices in Sponge Natural Product Studies: Revising Vouchers with Isomalabaricane Triterpenes

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