A-G.C.27: Improving comparative genomics with orthology uncertainty metrics
Authors
Yves Van de Peer
VIB-UGent Center for Plant Systems Biology
Zhen Li
VIB-UGent Center for Plant Systems Biology
Keywords
orthology, evolution, comparative genomics, orchid, gene loss
[sponser-meet-now-chat][/sponser-meet-now-chat]
Accurate identification of orthologs across species is critical for avoiding spurious gene-loss identification, inflated family expansions, and unreliable selection inferences in comparative genomics. Studies have shown that current orthology methods can vary widely in their orthology calls, but there remains no quantified method for determining the uncertainty of an ortholog group. Here, we develop an orthology uncertainty scoring system by integrating metrics including sequence similarity, synteny, and phylogenetic support. We benchmark our system with Dendrobium orchids, a genus known for morphological differences associated with gene loss, including transitions between lithophytic v.s. epiphytic lifestyles and photosynthetic strategies. Applying established orthology methods, we show that our uncertainty scoring scheme aids in spotting poorly supported orthology calls as well as identifying and confirming evolutionary events such as gene duplications and gene losses. Our work represents an important step forward in increasing the precision and certainty of evolutionary investigations into species history and adaptation.
Co-authors: Yves Van de Peer, Zhen Li
Contact Attendee
Warning: Attempt to read property "user_email" on string in /home/1276969.cloudwaysapps.com/ydbgzhdjeq/public_html/wp-content/plugins/my-conference-now/functions.php on line 2826