Landscape of gene transposition-duplication within the Brassicaceae family

Abstract

8Gene duplication, deletion, and transposition erode co-linearity between genomes over time, 9providing a substantial source of genomic structural variations. We developed CLfinder-OrthNet 10 pipeline to systematically trace gene duplication and transposition events by building networks based on 11 co-linearity among orthologs (OrthNets) from multiple closely related genomes. Using this pipeline, we 12 explored evolutionary events that result in erosion of co-linearity among six genomes in Brassicaceae, 13 including the model plant Arabidopsis thaliana and two extremophyte wild-relatives of Brassica crops 14 adapted to highly saline habitats. Out of 17,432 OrthNets derived from the six Brassicaceae genomes, 15 7,034 consisted of six co-linear orthologs, one from each genome, while the remaining included various 16 degrees and combinations of gene duplication, deletion, and transposition. We focused on 17 transposition-duplication (tr-d) events that lead to variations in both gene copy number and co-linearity. 32 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/236299 doi: bioRxiv preprint first posted online Dec. 18,

Cross species multi-omics reveals cell wall sequestration and elevated global transcription as mechanisms of boron tolerance in plants

“…This may be a result of a 15 kb transposition insertion in the upstream region adjacent to the SpBOR5 transcription start site (Oh et al, 2014). SpBOR5 and AtBOR5 exist as single copy genes and are co-linear except for the genomic insertion in S. parvula (Oh et al, 2014;Oh and Dassanayake, 2019). We demonstrated that SpBOR5 is an effective boron exporter ( Figure 2D) and propose that it is likely a key contributor to the underlying tolerance of S. parvula to excess boron (Figure 7).…”

“…When multiple spliced forms existed in A. thaliana, the longest version was considered. Orthologous gene pairs as best reciprocal hits between these two species were identified using the CLfinder-OrthNet pipeline with default settings (Oh and Dassanayake, 2019). To account for lineage-specific gene duplications in both species, orthologous gene pairs were searched reciprocally between the twospecies using BlastP with an e-value of 1e-5 and MMseqs2 (Steinegger and Söding, 2017) with an equivalent e-value cutoff.…”

Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed)

“…MCscan (as implemented in JCVI v. 1.1.7) 58 was used to compare syntenic depths between P. australis and other monocot genomes. SynMap 59 and CLfinder pipeline 60 detected co-linear paralog and ortholog pairs within the P. australis genome and between P. australis and monocot genomes, respectively. We estimated synonymous substitution rates at 4-fold degenerate sites using codeml 61 as described previously 60 .…”

Divergence in a stress regulatory network underlies differential growth control

“…Differentially expressed genes were estimated using DESeq2 51 . For comparative analyses, primary protein-coding gene models from the four species were compared using CLfinder pipeline 52 with MMSeqs2 53 as the aligner, to identify ortholog pairs and groups between pairs of species as well as for all four species. Gene Ontology (GO) annotation for A. thaliana was obtained on July 1st, 2020, from the GO consortium (http://geneontology.org/).…”

“…Protein-coding gene models from each species were paired with their best homologs in other species. Pairs of homologs were organized into OrthNet, each OrthNet representing orthologs likely derived from a single ancestral locus (Oh and Dassanayake, 2019). Within each OrthNet, a quartet of orthologs unambiguously find each other as reciprocal best homologs is defined as “all 1-to-1 ortholog group (OG)” (red dashed box).…”