Landscape of gene transposition–duplication within the Brassicaceae family

Abstract

We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition–duplication (tr–d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr–d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr–d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. These were derived from older tr–d events and had a higher chance of being expressed. We also found an enrichment of tr–d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr–d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr–d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3 that relate to their adaptive evolution. CLfinder-OrthNet provides a flexible toolkit to compare gene order, visualize evolutionary paths among orthologues as networks, and identify gene loci that share an evolutionary history.

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

“…australis and other monocot genomes. SynMap (Lyons & Freeling, 2008 ) and CLfinder pipeline (Oh & Dassanayake, 2019 ) were used to detect colinear paralogue and orthologue pairs within the P . australis genome and between P .…”

“…MCscan (as implemented in JCVI v. 1.1.7) (Tang et al, 2008) was used to compare syntenic depths between P. australis and other monocot genomes. SynMap (Lyons & Freeling, 2008) and CLfinder pipeline (Oh & Dassanayake, 2019) were used to detect colinear paralogue and orthologue pairs within the P. australis genome and between P. australis and monocot genomes, respectively.…”

“…We estimated synonymous substitution rates at four-fold degenerate sites using codeml (Yang, 1997) as described previously (Oh & Dassanayake, 2019). We detected orthologue groups among representative gene models of P. australis and other monocot genomes using OrthoFinder (v. 2.2.7) (Emms & Kelly, 2019) and MMseqs2 (Steinegger & Söding, 2017) and subsequently identified P. australis orthologue groups that are "conserved" and "duplicated" in orthologue copy numbers compared to other monocot species as detailed in Supporting Information Methods.…”

Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems?

“…Most of these genomic structural variations also affect gene copy number variation (CNV), which, for decades, has been proposed as a major driver of adaptation to new environments (Ohno, 1970;DeBolt, 2010). Table 2 lists genes associated with stress responses in Arabidopsis that show CNV unique to S. parvula and E. salsugineum based on a network analysis using synteny information from Brassicaceae genomes (Oh and Dassanayake, 2018).…”

“…The selected duplication events were not detected in other Brassicaceae lineage I and II genomes in a multispecies comparison including Arabidopsis, Arabidopsis lyrata, Capsella rubella, and Sisymbrium irio genomes (selected subset from Oh and Dassanayake, 2018 genomic and transcriptomic analyses coupled with functional genetic studies using not just Arabidopsis but also the halophytes could lead to the discovery of naturally selected, stress-adaptive mechanisms.…”