A Complete Theoretical Framework for Inferring Horizontal Gene Transfers Using Partial Order Sets

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2023 Mar 24

PMID 36961781

Authors

Nahla A Belal

Lenwood S Heath

Affiliations

Soon will be listed here.

Abstract

We present a method for detecting horizontal gene transfer (HGT) using partial orders (posets). The method requires a poset for each species/gene pair, where we have a set of species S, and a set of genes G. Given the posets, the method constructs a phylogenetic tree that is compatible with the set of posets; this is done for each gene. Also, the set of posets can be derived from the tree. The trees constructed for each gene are then compared and tested for contradicting information, where a contradiction suggests HGT.

References

Boc A, Philippe H, Makarenkov V . Inferring and validating horizontal gene transfer events using bipartition dissimilarity. Syst Biol. 2010; 59(2):195-211. DOI: 10.1093/sysbio/syp103. View

Chan Y, Ranwez V, Scornavacca C . Exploring the space of gene/species reconciliations with transfers. J Math Biol. 2014; 71(5):1179-209. DOI: 10.1007/s00285-014-0851-2. View

Sanchez-Soto D, Aguero-Chapin G, Armijos-Jaramillo V, Perez-Castillo Y, Tejera E, Antunes A . ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes. Genes (Basel). 2020; 11(7). PMC: 7397055. DOI: 10.3390/genes11070756. View

Jin G, Nakhleh L, Snir S, Tuller T . Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Mol Biol Evol. 2006; 24(1):324-37. DOI: 10.1093/molbev/msl163. View

Abby S, Tannier E, Gouy M, Daubin V . Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics. 2010; 11:324. PMC: 2905365. DOI: 10.1186/1471-2105-11-324. View

Nguyen M, Ekstrom A, Li X, Yin Y . HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes. Toxins (Basel). 2015; 7(10):4035-53. PMC: 4626719. DOI: 10.3390/toxins7104035. View

Bapteste E, Walsh D . Does the 'Ring of Life' ring true?. Trends Microbiol. 2005; 13(6):256-61. DOI: 10.1016/j.tim.2005.03.012. View

Bailey C, Fain M, Houde P . On conditioned reconstruction, gene content data, and the recovery of fusion genomes. Mol Phylogenet Evol. 2006; 39(1):263-70. DOI: 10.1016/j.ympev.2005.11.020. View

Podell S, Gaasterland T . DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 2007; 8(2):R16. PMC: 1852411. DOI: 10.1186/gb-2007-8-2-r16. View

10.

Cardona G, Pons J, Rossello F . A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. Algorithms Mol Biol. 2015; 10:28. PMC: 4683721. DOI: 10.1186/s13015-015-0059-z. View

11.

Rujan T, Martin W . How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet. 2001; 17(3):113-20. DOI: 10.1016/s0168-9525(00)02209-5. View

12.

Lake J, Rivera M . Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol Biol Evol. 2004; 21(4):681-90. DOI: 10.1093/molbev/msh061. View

13.

Layeghifard M, Peres-Neto P, Makarenkov V . Inferring explicit weighted consensus networks to represent alternative evolutionary histories. BMC Evol Biol. 2013; 13:274. PMC: 3898054. DOI: 10.1186/1471-2148-13-274. View

14.

Than C, Rosenberg N . Consistency properties of species tree inference by minimizing deep coalescences. J Comput Biol. 2011; 18(1):1-15. DOI: 10.1089/cmb.2010.0102. View

15.

Snir S, Trifonov E . A novel technique for detecting putative horizontal gene transfer in the sequence space. J Comput Biol. 2010; 17(11):1535-48. DOI: 10.1089/cmb.2010.0095. View

16.

Bansal M, Wu Y, Alm E, Kellis M . Improved gene tree error correction in the presence of horizontal gene transfer. Bioinformatics. 2014; 31(8):1211-8. PMC: 4393519. DOI: 10.1093/bioinformatics/btu806. View

17.

Mallet J, Besansky N, Hahn M . How reticulated are species?. Bioessays. 2015; 38(2):140-9. PMC: 4813508. DOI: 10.1002/bies.201500149. View

18.

Bansal M, Kellis M, Kordi M, Kundu S . RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss. Bioinformatics. 2018; 34(18):3214-3216. PMC: 6137995. DOI: 10.1093/bioinformatics/bty314. View

19.

Ponting C . Plagiarized bacterial genes in the human book of life. Trends Genet. 2001; 17(5):235-7. DOI: 10.1016/s0168-9525(01)02282-x. View

20.

Nakhleh L, Warnow T, Linder C, St John K . Reconstructing reticulate evolution in species-theory and practice. J Comput Biol. 2005; 12(6):796-811. DOI: 10.1089/cmb.2005.12.796. View