Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Rancurel, Corinne; Legrand, Ludovic; Danchin, Etienne G. J.

doi:10.20944/preprints201708.0107.v1

Cited by 22 publications

(24 citation statements)

References 36 publications

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“…Putative HGT events in X. index and L. elongatus were detected by the Alienness software [ 44 , 45 ] which calculates an Alien Index (AI) as initially described in [ 46 ]. Briefly, all predicted proteins were compared against the National Center for Biotechnology Information (NCBI) non-redundant library (nr) using BLASTp [ 32 ] with an E-value threshold of 1E −3 and no low-complexity filtering.…”

Section: Methodsmentioning

confidence: 99%

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

Danchin

Perfus‐Barbeoch

Rancurel

et al. 2017

Genes

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Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.

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Section: Methodsmentioning

confidence: 99%

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

Danchin

Perfus‐Barbeoch

Rancurel

et al. 2017

Genes

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“…Some genes, such as virulence factors are carried by mobile elements. Furthermore, genes may be able to persist in MGEs through hitch-hiking with beneficial genes or alleles ensuring high frequencies via selection of MGEs [46] and transfer between organisms [47]. To evaluate the direct effects of CRISPR-Cas system on HGT, we analyzed the variation of unique genes of strains with complete, incomplete, and none CRISPR-Cas systems in the B. cereus group.…”

Section: Strains With Intact Crispr-cas System Contain Restricted Nicmentioning

confidence: 99%

The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments

et al. 2020

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CRISPR-Cas systems are considered as barriers to horizontal gene transfer (HGT). However, the influence of such systems on HGT within species is unclear. Also, little is known about the impact of CRISPR-Cas systems on bacterial evolution at the population level. Here, using Bacillus cereus sensu lato as model, we investigate the interplay between CRISPR-Cas systems and HGT at the population scale. We found that only a small fraction of the strains have CRISPR-Cas systems (13.9% of 1871), and most of such systems are defective based on their gene content analysis. Comparative genomic analysis revealed that the CRISPR-Cas systems are barriers to HGT within this group, since strains harboring active systems contain less mobile genetic elements (MGEs), have lower fraction of unique genes and also display limited environmental distributions than strains without active CRISPR-Cas systems. The introduction of a functional CRISPR-Cas system into a strain lacking the system resulted in reduced adaptability to various stresses and decreased pathogenicity of the transformant strain, indicating that B. cereus group strains could benefit from inactivating such systems. Our work provides a large-scale case to support that the CRISPR-Cas systems are barriers to HGT within species, and that in the B. cereus group the inactivation of CRISPR-Cas systems correlated with acquisition of MGEs that could result in better adaptation to diverse environments.

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“…Nevertheless, there are several methods to detect xenologs in a genome that use sequence features rather then phylogenetic reconstructions, see e.g. [41,42]. In this contribution we focus on the mathematical properties of the xenology relation X.…”

Section: Introductionmentioning

confidence: 99%

Reconstructing gene trees from Fitch’s xenology relation

et al. 2018

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Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains within the ancestral lineage. Hence xenology is more precisely thought of as a non-symmetric relation: y is xenologous to x if y has been horizontally transferred at least once since it diverged from the least common ancestor of x and y. We show that xenology relations are characterized by a small set of forbidden induced subgraphs on three vertices. Furthermore, each xenology relation can be derived from a unique least-resolved edge-labeled phylogenetic tree. We provide a linear-time algorithm for the recognition of xenology relations and for the construction of its least-resolved edge-labeled phylogenetic tree. The fact that being a xenology relation is a heritable graph property, finally has far-reaching consequences on approximation problems associated with xenology relations.

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Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Cited by 22 publications

References 36 publications

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments

Reconstructing gene trees from Fitch’s xenology relation

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