Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage

Lateral gene transfer (LGT) is the movement of DNA between organism without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor’s genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics.
We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses.
We detect 168 laterally acquired genes in the five reference genomes [32-100 per genome]. Exponential decay models indicate that the rate of LGT acquisitions [6-28 per Ma] and subsequent losses [11-24% per Ma] varied significantly among lineages. Laterally acquired genes were lost at a high...,  Nucleotide alignments, Maximum likelihood phylogenetic trees, genome assemblies and annotations. Please see manuscript for full details., , three zipped files:

[1] Alignments.zip

Fasta file alignments for candidate lateral gene transfers (LGTs) identified in Alloteropsis genomes. these are divided into Primary (n=108) and Secondary (n=71) depending on how they were identified (please see publication for further details)

[2] Phylogenetic\_trees.zip

These are maximum likelihood phylogenetic trees inferred from alignments (also uploaded) for candidate LGTs. Again, divided into Primary (n=108) and Secondary (n=71) depending on how they were identified (please see publication for further details)

[3] Assembly and annotation

This includes 10 files, genome assembly (.fasta/.fa) and annotations (.gff) for five Alloteropsis accessions:

AANG\_UGA4
AUS1
RSA5-3
TAN1-04B
ZAM1505-10

(for full assembly methods please see publication)