Horizontal Gene Transfer Involved in the Convergent Evolution of the Plasmid-Encoded Enantioselective 6-Hydroxynicotine Oxidases

Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer (HGT) due to their unexpectedly high homology. Here we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of HGT. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

Download Full-text

Examining marginal sequence similarities between bacterial type III secretion system components and Trypanosoma cruzi surface proteins: horizontal gene transfer or convergent evolution?

Frontiers in Genetics ◽

10.3389/fgene.2013.00143 ◽

2013 ◽

Cited By ~ 1

Author(s):

Silva

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Trypanosoma Cruzi ◽

Type Iii Secretion ◽

Convergent Evolution ◽

Secretion System ◽

Surface Proteins ◽

System Components ◽

Bacterial Type ◽

Sequence Similarities

Download Full-text

A Comprehensive Phylogenetic Analysis of the Serpin Superfamily

Molecular Biology and Evolution ◽

10.1093/molbev/msab081 ◽

2021 ◽

Author(s):

Matthew A Spence ◽

Matthew D Mortimer ◽

Ashley M Buckle ◽

Bui Quang Minh ◽

Colin J Jackson

Keyword(s):

Phylogenetic Analysis ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Convergent Evolution ◽

Alternative Hypothesis ◽

Structural Alignment ◽

High Homology ◽

Physiological Processes ◽

New Directions ◽

Hub Proteins

Abstract Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central “hub” of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of horizontal gene transfer. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.

Download Full-text

Homoplasy as an Auxiliary Criterion for Species Delimitation

Microorganisms ◽

10.3390/microorganisms9020273 ◽

2021 ◽

Vol 9 (2) ◽

pp. 273

Author(s):

Angela Conti ◽

Debora Casagrande Pierantoni ◽

Vincent Robert ◽

Gianluigi Cardinali ◽

Laura Corte

Keyword(s):

New Species ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Species Delimitation ◽

Convergent Evolution ◽

Simulated Data ◽

Single Element ◽

Phylogenetic Reconstructions ◽

Taxonomic Markers ◽

Auxiliary Test

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases—as expected—with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.

Download Full-text