Abstract Detail

Angiosperms353: A new essential tool for plant systematics

Frost, Laura [1], Santamaria, Daniel [2], Lagomarsino, Laura [3].

Cabinet to table: an artisanal approach to get the most out of Angiosperm-353 data from herbarium specimens.

The Angiosperms-353 universal bait set offers quick and cost effective target enrichment relative to custom probe sets, is useful in clades for which genome/transcriptome data from which to design custom probes are scarce, and produces datasets that can be easily combined with those from other Angiosperms-353 studies. We set out to generate the first phylogenetic hypotheses for two understudied, Neotropical genera, Freziera(Pentaphylacaceae; ca.75 spp.) and Otoba(Myristicaceae; 10-13 spp.), using Angiosperms-353 with DNA extracted from herbarium specimens. Expected drawbacks to this approach were (1) large amounts of missing data due to degraded DNA from herbarium specimens and the potential for poor matches between samples and the universal probes, and (2) low variability in targeted genes at the genus level. A third difficulty, which is becoming increasingly acknowledged in genomic-level datasets, was cryptic paralogy, or unidentified copies of the single-copy target genes. We explore different methods of data extraction and processing to overcome the challenges of low variability, which was especially problematic in Otoba, and cryptic paralogy, which was common in Frezeria, in Angiosperm-353 datasets. We compared the ability of different pipelines, HybPiper and Phyluce, to recover multiple copies within genes. For this dataset, we found that Phyluce had the advantage for recovering and parsing paralogs, but a disadvantage for time spent in data processing. We also explored automated data cleaning versus visual cleaning to reduce noise in phylogenetic signal caused by assembly and alignment error; noise which can quickly drown signal when the number of informative sites is low. Careful curation of datasets through correction of assembly and alignment error, especially among closely related taxa, as well as parsing copies is important as these can affect phylogenetic inference and, therefore, interpretations of evolutionary patterns and processes.

1 - Louisiana State University, Department Of Biological Sciences, 202 Life Sciences Building, Baton Rouge, LA, 70803, United States
2 - Louisiana State University, Department of Biological Sciences, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
3 - Louisiana State University, Dept Of Biological Sciences, 103 Life Sciences Building, Baton Rouge, LA, 70803, United States

Keywords:
Angiosperms-353
museomics
Freziera (Pentaphylacaceae)
Otoba (Myristicaceae)
Neotropics
paralogy
Hybpiper
Phyluce.

Presentation Type: Symposium Presentation
Session: SY4, Angiosperms353: A new essential tool for plant systematics
Location: Virtual/Virtual
Date: Thursday, July 30th, 2020
Time: 11:30 AM
Number: SY4004
Abstract ID:585
Candidate for Awards:None