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. 2015 Apr 6;3(4):apps.1400115.
doi: 10.3732/apps.1400115. eCollection 2015 Apr.

MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes

Srikar Chamala  1 , Nicolás García  2 , Grant T Godden  3 , Vivek Krishnakumar  4 , Ingrid E Jordon-Thaden  5 , Riet De Smet  6 , W Brad Barbazuk  7 , Douglas E Soltis  8 , Pamela S Soltis  9
Affiliations

MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes

Srikar Chamala et al. Appl Plant Sci. .

Abstract

Premise of the study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited.

Methods and results: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales.

Conclusions: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.

Keywords: data mining; introns; marker development; next-generation sequencing; phylogenetics; single-copy nuclear genes; transcriptomes.

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Figures

Fig. 1.
Fig. 1.
Filtering steps performed by MarkerMiner 1.0 to identify single-copy nuclear genes from angiosperm transcriptome assembly input. Best (primary) alignments are identified with a star, and secondary alignments are identified with a diamond.
Fig. 2.
Fig. 2.
Additional data processing and output steps performed by MarkerMiner 1.0.
Fig. 3.
Fig. 3.
Alignment output produced by MarkerMiner 1.0, including multiple sequence alignments and reference CDS profile alignments for single-copy nuclear loci. The alignment output is useful for assessing the phylogenetic utility of individual loci, predicting putative intron sizes and locations, and developing primers or probes for targeted sequencing.
Fig. 4.
Fig. 4.
MarkerMiner 1.0 results for four test cases involving SCN locus discovery at different phylogenetic scales: e.g., interfamilial (Lamiales: 77 transcriptomes), intrafamilial (Amaryllidaceae s.l.: 7 transcriptomes), and intergeneric (Solanum L. and Draba L.: 6 transcriptomes each). Three graphs illustrate the following for each of the test cases: (A) the total number of detected SCN loci, (B) the distribution of SCN loci detected per taxon, and (C) the distribution of shared SCN loci detected across sampled accessions.
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