Abstract Detail

Phylogenomics

Malley, Claire [1], Johnson, Matthew [2], Goffinet, Bernard [3], Shaw, A Jonathan [4], Wickett, Norm [5].

Circumscribing a core set of conserved, orthologous genes for moss phylogenetics.

Often, the first step in a phylogenetic analysis using hundreds of nuclear genes is to determine orthologous clusters from a pool of thousands of candidate gene families. The determination of orthology is a critical step in that it allows us to circumscribe a set of genes that we infer to have arisen by speciation, which may be preferable for reconstructing species relationships. Whenever possible, orthologous gene families (often called single copy genes) should be circumscribed using the inferred protein sets of sequenced genomes, mitigating the effects of processes that may confound a clustering analysis using other types of data, for example transcriptomes (alternative splicing, lack of expression, incompletely assembled transcripts etc.). However, under-studied or non-model lineages are often characterized by a lack of complete genome sequences and, instead, orthologous gene families must be described using transcriptome data and, if possible, any available genomic resources. In addition to a diversity of input data, there are several different methods available to circumscribe orthologs (e.g. OrthoFinder, Proteinortho). Here, we explore how the identification of orthologous gene families differs among methods and among program-specific parameters using a set of six transcriptomes and a single genome (Physcomitrella patens), allowing us to identify single-copy gene families that are robust to changes in both program and parameters. We then discuss the applicability of the identified conserved, orthologous genes to the reconstruction of the back-bone phylogeny of mosses using an additional 55 transcriptomes.

1 - Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, Illinois, 60022, United States
2 - Chicago Botanic Garden, Plant Sciences, 1000 Lake Cook Road, Glencoe, IL, 60626, United States
3 - University of Connecticut, Ecology and Evolutionary Biology, Storrs, CT, 06269, USA
4 - 130 Science Drive, Box 90338, Durham, NC, 27708, USA
5 - Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Road, Glencoe, IL, 60022, USA

Keywords:
phylogenomics
transcriptomes
Mosses
Bryophytes
Bioinformatics.

Presentation Type: Oral Paper
Session: 38, Phylogenomics III
Location: 204/Savannah International Trade and Convention Center
Date: Wednesday, August 3rd, 2016
Time: 8:45 AM
Number: 38004
Abstract ID:723
Candidate for Awards:None