A Protocol for Horizontally Acquired Metabolic Gene Detection in Algae

Document Type

Article

Publication Date

1-1-2022

Publication Title

Methods in molecular biology (Clifton, N.J.)

Keywords

JGM, Comparative genomics, Horizontal gene transfer, Phylogenetic reconstruction

JAX Source

Methods Mol Biol . 2022:2396:61-69.

Volume

2396

First Page

61

Last Page

69

PMID

34786676

DOI

10.1007/978-1-0716-1822-6_6

Abstract

Horizontal gene transfer (HGT) or lateral gene transfer (LGT), the exchange of genetic materials among organisms by means of other than parent-to-offspring (vertical) inheritance, plays a major role in prokaryotic genome evolution, facilitating adaptation of prokaryotes to changes in the environment. Phylogenetic methods have been frequently invoked to catalog horizontally acquired genes; however, these methods are often constrained by the paucity of sequenced genomes of close relatives (and even distant relatives) for a robust analysis and reliable inference. In this chapter, we describe a HGT quantification protocol that exploits the complementary strengths of the integrative segmentation and clustering method and the comparative genomics approach to identify foreign genes. Users can use this pipeline in combination with phylogenetic tree reconstruction to identify foreign genes that are supported by multiple lines of evidence, that is, atypical composition, atypical distribution in close relatives, and aberrant phylogenetic pattern.

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