Abstract Detail

Phylogenomics

Chamala, Srikar [1], Godden, Grant T. [2], Garcia, Nicolas [3], Jordon-Thaden, Ingrid [4], Soltis, Douglas E. [5], SOLTIS, PAMELA S. [5].

MarkerMiner 1.0: A New Pipeline and Tool for Phylogenetic Marker Development Using Angiosperm Transcriptomes.

The availability of new molecular techniques, next-generation sequencing (NGS) technologies, and computational tools has recently revolutionized the field of plant molecular systematics. We have acquired the ability to quickly generate and assemble genome-scale data resources for any taxonomic group of interest, and with relatively little financial investment. Our improved access to these new data resources presents exciting opportunities for researchers to develop hundreds or potentially thousands of informative, taxon-specific loci from both organellar and nuclear genomes—large, multilocus data sets that can potentially resolve relationships at any phylogenetic depth. The discovery of single-copy nuclear (SCN) loci from NGS data (e.g., low-coverage genome skimming and transcriptome data), in particular, has recently emerged as an exciting area of development within the plant systematics community. In fact, a few pioneering studies have reported great success in developing large sets of SCN loci with elaborately designed pipelines. However, as many researchers may have recognized, the discovery of orthologous loci from NGS data constitutes a complex, multi-step process that requires advanced bioinformatics training and skills for pipeline development. Unfortunately, there are no publicly available marker development pipelines for use by the larger research community, and many researchers do not yet possess the advanced bioinformatic skills necessary to navigate this complex process. To address this issue, we developed MarkerMiner 1.0, a new tool backed by a new bioinformatic pipeline for discovery of known SCN loci for phylogenetic applications. MarkerMiner’s easy-to-use graphical user interface allows researchers to input assembled transcriptome data from any angiosperm group of interest, and the software outputs a detailed report that includes: a gene identifier, a gene single-copy status, a gene functional category annotation, and the number of gene orthologues recovered across all input samples. Moreover, MarkerMiner streamlines downstream locus development processes (e.g., primer or probe design) by outputting both gene alignments and gene profile alignments with a user-specified reference genome. These added features allow researchers to assess the phylogenetic utility of each locus and to identify putative intron-exon boundaries, respectively. Preliminary tests with MarkerMiner and transcriptome data from the One Thousand Plants Project (1kp) yielded hundreds to thousands of SCN loci in our tests with five independent use cases. Our results are encouraging and clearly demonstrate the potential benefits of employing SCN loci in phylogenetic studies of angiosperms.

1 - University of Florida, Department of Biology, 407 Cancer and Genetics Research Complex, Gainesville, FL, 32611, USA
2 - University of Florida, Department of Biology and Florida Museum Of Natural History, Dickinson Hall, Gainesville, FL, 32611-7800, USA
3 - University Of Florida, Florida Museum Of Natural History, Dickinson Hall, Gainesville, FL, 32611, USA
4 - Bucknell University, Biological Sciences, 203 Biology Building, Lewisburg, PA, 17837, USA
5 - University of Florida, Florida Museum of Natural History, PO Box 117800, Gainesville, FL, 32611, USA

Keywords:
single copy nuclear genes
marker discovery
transcriptomes
phylogenomics
next-generation sequencing
angiosperms
Bioinformatics.

Presentation Type: Oral Paper:Papers for Topics
Session: 43
Location: Evergreen/Grove
Date: Wednesday, July 30th, 2014
Time: 1:45 PM
Number: 43002
Abstract ID:556
Candidate for Awards:None