Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac062
Abstract: MOTIVATION Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software,… read more here.
Keywords: phylogenetic encounters; reconciliation; host symbiont; thirdkind displaying ... See more keywords
Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny
Sign Up to like & getrecommendations! Published in 2019 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2018.2838667
Abstract: The aim of this paper is to explore the robustness of the parsimonious host-symbiont tree reconciliation method under editing or small perturbations of the input. The editing involves making different choices of unique symbiont mapping… read more here.
Keywords: robustness parsimonious; host symbiont; reconciliation; host ... See more keywords
Variation and asymmetry in host-symbiont dependence in a microbial symbiosis
Sign Up to like & getrecommendations! Published in 2018 at "BMC Evolutionary Biology"
DOI: 10.1186/s12862-018-1227-9
Abstract: BackgroundSymbiosis is a major source of evolutionary innovation and, by allowing species to exploit new ecological niches, underpins the functioning of ecosystems. The transition from free-living to obligate symbiosis requires the alignment of the partners’… read more here.
Keywords: dependence; variation; symbiosis; symbiont dependence ... See more keywords
Elucidation of host and symbiont contributions to peptidoglycan metabolism based on comparative genomics of eight aphid subfamilies and their Buchnera
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DOI: 10.1371/journal.pgen.1010195
Abstract: Pea aphids (Acyrthosiphon pisum) are insects containing genes of bacterial origin with putative functions in peptidoglycan (PGN) metabolism. Of these, rlpA1-5, amiD, and ldcA are highly expressed in bacteriocytes, specialized aphid cells that harbor the… read more here.
Keywords: metabolism; host symbiont; loss; buchnera ... See more keywords
SeqDeχ: A Sequence Deconvolution Tool for Genome Separation of Endosymbionts From Mixed Sequencing Samples
Sign Up to like & getrecommendations! Published in 2019 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2019.00853
Abstract: In recent years, the advent of NGS technology has made genome sequencing much cheaper than in the past; the high parallelization capability and the possibility to sequence more than one organism at once have opened… read more here.
Keywords: tool; seqdex; host symbiont; deconvolution ... See more keywords
Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses
Sign Up to like & getrecommendations! Published in 2022 at "Life"
DOI: 10.3390/life12030443
Abstract: Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the… read more here.
Keywords: reconciliation; tree reconciliation; host symbiont; reconciliation methods ... See more keywords