A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees

López-Fernández, Hugo; Duque, Pedro; Henriques, Sílvia F.; Vázquez, Noé; Fdez-Riverola, Florentino; Vieira, Cristina; Reboiro-Jato, Miguel; Vieira, Jorge

doi:10.1007/978-3-319-98702-6_11

Cited by 5 publications

(22 citation statements)

References 12 publications

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Section: Resultsmentioning

confidence: 99%

“…The implementation of a fast an efficient protocol for the identification of GULO gene in annotated genomes led to the identification of this gene in 118 species, in groups such as the Anthozoa (non-Bilaterian), Araneae, Priapulida, Brachiopoda and Gastropoda (Protostomians) [17]. This result motivated us to use non-annotated genomes of further non-Bilateria and Protostomia species that belong to phylogenetic groups that were not well represented in [17]. Furthermore, since many taxonomic groups are represented by a reduced number of annotated species genomes only, we decided to perform our own annotations using these genomes to avoid loss of information that could arise from poor annotations that were eventually removed in [17].…”

Section: Resultsmentioning

confidence: 99%

“…Although Vitamin C could be detected in many species [10, 13–16], most Protostomes were thought not to have a GULO gene. Nevertheless, recently, the GULO gene has been identified in the annotated genomes of five Araneae, Priapulida, Brachiopoda and Gastropoda species [17]. Therefore, the GULO gene has not been completely lost in Protostomian species.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, the GULO gene has not been completely lost in Protostomian species. There are, however, three Protostomian lineages where a GULO gene has not been detected, although a large number of genomes has been analysed, namely the Insects (116 genomes), Nematoda (35 genomes) and Platyhelminthes (nine genomes) [17]. In non-Bilateria, the GULO gene has been found in Anthozoan and Placozoan species [10, 17], showing that, in animals, having a GULO gene is the ancestral state.…”

Section: Introductionmentioning

confidence: 99%

“…There are, however, three Protostomian lineages where a GULO gene has not been detected, although a large number of genomes has been analysed, namely the Insects (116 genomes), Nematoda (35 genomes) and Platyhelminthes (nine genomes) [17]. In non-Bilateria, the GULO gene has been found in Anthozoan and Placozoan species [10, 17], showing that, in animals, having a GULO gene is the ancestral state. In this work we present evidence that GULO is also present in the Myxozoa (non-Bilaterian), Acari and Annelida groups (Protostomian), and thus that GULO is present in most non-Bilaterian and Protostomian lineages.…”

Section: Introductionmentioning

confidence: 99%

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Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species

et al. 2019

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Background L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase ( GULO ), is lost. Since Protostomes were until recently thought not to have a GULO gene, they were considered to be auxothrophs for Vitamin C. Results By performing phylogenetic analyses with tens of non-Bilateria and Protostomian genomes, it is shown, that a GULO gene is present in the non-Bilateria Placozoa, Myxozoa (here reported for the first time) and Anthozoa groups, and in Protostomians, in the Araneae family, the Gastropoda class, the Acari subclass (here reported for the first time), and the Priapulida, Annelida (here reported for the first time) and Brachiopoda phyla lineages. GULO is an old gene that predates the separation of Animals and Fungi, although it could be much older. We also show that within Protostomes, GULO has been lost multiple times in large taxonomic groups, namely the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia groups, a pattern similar to that reported for Vertebrate species. Nevertheless, we show that Drosophila melanogaster seems to be capable of synthesizing L-ascorbate, likely through an alternative pathway, as recently reported for Caenorhabditis elegans . Conclusions Non-Bilaterian and Protostomians seem to be able to synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule. Electronic supplementary material The online version of this article (10.1186/s12862-019-1454-8) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%