Systematic errors in orthology inference and their effects on evolutionary analyses

Natsidis, Paschalis; Kapli, Paschalia; Schiffer, Philipp H.; Telford, Maximilian J.

doi:10.1016/j.isci.2021.102110

Cited by 34 publications

(45 citation statements)

References 40 publications

(54 reference statements)

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“…2c). Because other data have shown the monophyly of Xenacoelomorpha to be robust, we interpret this result as being the result of systematic error caused by a high rate of gene loss or by orthologs being incorrectly scored as missing due to higher rates of sequence evolution in acoelomorphs 26 .…”

Section: The Genome Of a Potential Symbiont Chlamydiamentioning

confidence: 92%

The slowly evolving genome of the xenacoelomorph wormXenoturbella bocki

Schiffer

Natsidis

Leite

et al. 2022

Preprint

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The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data, which can help to elucidate phylogenetic relationships and provide important comparative data, remain sparse for early branching bilaterians. Here we assemble and analyse the genome of the simple, marine xenacoelomorph Xenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly of X. bocki has a size of ~110 Mbp in 18 chromosome like scaffolds, with repeat content, and intron, exon and intergenic space comparable to other bilaterian invertebrates. We find X. bocki to have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude that X. bocki has a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.

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Section: The Genome Of a Potential Symbiont Chlamydiamentioning

confidence: 92%

The slowly evolving genome of the xenacoelomorph wormXenoturbella bocki

Schiffer

Natsidis

Leite

et al. 2022

Preprint

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“…However, we observed good congruence across datasets over the topology in Fig. 2 (Genome Gene Content), indicating that errors induced by ortho-and homogroup misidentifications were negligible (contra Natsidis et al, 2021).…”

Section: Discussionmentioning

confidence: 74%

“…However, we observed good congruence across datasets over the topology in Fig. 2 (Genome Gene Content), indicating that errors induced by misidentifications of orthogroups were negligible (contra 42 ), while homogroup-based topologies were less congruent mostly when high inflation values were used for the predictions.…”

Section: Discussionmentioning

confidence: 78%

“…We assembled a large number of new gene content datasets (see Methods, Fig. 1) to extensively test the effect of different parameter combinations when identifying homogroups and orthogroups, because this crucial step remains a challenge (Frech & Chen, 2010;Lunter et al, 2008) and may influence the outcome of the downstream phylogenetic analysis (Natsidis et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

Juravel

Porras

Höhna

et al. 2021

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An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the “Superphylum” Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

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“…1H) (Wasik, et al 2015; Wudarski, et al 2017). It is possible that the large number of specific orthology groups in M. lignano is associated with the divergence of these duplicated genes (Holland, et al 2017; Natsidis, et al 2021).…”

Section: Resultsmentioning

confidence: 99%

Genome assembly of the polyclad flatworm Prostheceraeus crozieri

Leite

Piovani

Telford

2022

Preprint

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Polyclad flatworms are widely thought to be one of the least derived of the flatworm classes and, as such, are well placed to investigate evolutionary and developmental features such as spiral cleavage and larval diversification lost in other platyhelminths. Prostheceraeus crozieri, formerly Maritigrella crozieri, is an emerging model polyclad flatworm that already has some useful transcriptome data but, to date, no sequenced genome. We have used high molecular weight DNA extraction and long read PacBio sequencing to assemble the highly repetitive (67.9%) P. crozieri genome (2.07 Gb). We have annotated 43,325 genes, with 89.7% BUSCO completeness. Perhaps reflecting its large genome, introns were considerably larger than other free-living flatworms, but evidence of abundant transposable elements suggests genome expansion has been principally via transposable elements activity. This genome resource will be of great use for future developmental and phylogenomic research.

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Systematic errors in orthology inference and their effects on evolutionary analyses

Cited by 34 publications

References 40 publications

The slowly evolving genome of the xenacoelomorph wormXenoturbella bocki

The slowly evolving genome of the xenacoelomorph wormXenoturbella bocki

Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

Genome assembly of the polyclad flatworm Prostheceraeus crozieri

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