Create your own conference schedule! Click here for full instructions

Abstract Detail


Battenberg, Kai [1], Lee, Ernest K. [2], Chiu, Joanna C. [2], Berry, Alison M. [1], Potter, Daniel [3].

Orthologfinder: A newly developed automated orthology prediction tool -A case study analyzing the transcriptomes of actinorhizal plants-.

Identifying orthologous genes is an initial step required for phylogenetics. However, in silico orthology prediction tools often require large computational resources only available on high-performance computing clusters. Here we present Orthologfinder, an orthology prediction tool with accuracy comparable to other published tools that requires only a desktop computer. The low resource requirement is achieved by (1) taking a gene-by-gene approach rather than analyzing all genes at once, and there by (2) minimizing the number of sequences analyzed at a time. With high-throughput sequencing, unprecedented number of genes from non-model organisms is available with increasing need for clear information about their orthologies. Orthologfinder is not only fast and accurate as an orthology prediction tool, but also gives researchers flexibility in the number of genes analyzed at a time without a high-performance computing cluster. Testing Orthologfinder with three datasets, which represented three phyla with different ranges of species diversity and different number of genomes included, we found that the predicted orthologs were highly similar to the predictions made by other published orthology prediction tools. Median CPU time for orthology prediction per gene by executing Orthologfinder on a desktop computer was de novo assembled transcriptomes of two actinorhizal (engaging in nitrogen-fixing root nodule symbioses with Actinobacteria) plant species, Ceanothus thyrsiflorus and Datisca glomerata. In a search including genomes of angiosperms across the four Rosid orders comprising the nitrogen-fixing clade (Fabales, Rosales, Cucurbitales, and Fagales), Orthologfinder found that orthologs of most of the genes known to be involved in the process of root nodule symbiosis establishment in legumes are also present in C. thyrsiflorus and D. glomerata. Our results based on the predicted orthology and gene expression patterns support the hypothesis that the root nodules of C. thyrsiflorus and D. glomerata are homologous to those of the model legume Medicago truncatula.

Log in to add this item to your schedule

1 - University of California, Davis, Department of Plant Sciences, One Shields Avenue, Davis, CA, 95616, USA
2 - University of California, Davis, Department of Entomology and Nematology, One Shields Avenue, Davis, CA, 95616, USA
3 - University Of California Davis, DEPARTMENT OF PLANT SCIENCES MAIL STOP 2, One Shields Avenue, Davis, CA, 95616-8780, USA


Presentation Type: Poster
Session: P, Phylogenomics
Location: Exhibit Hall/Omni Hotel
Date: Monday, June 26th, 2017
Time: 5:30 PM This poster will be presented at 5:30 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PPH001
Abstract ID:164
Candidate for Awards:None

Copyright © 2000-2017, Botanical Society of America. All rights reserved