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

Chamala, Srikar; Garcı́a, N.; Godden, Grant T.; Krishnakumar, Vivek; Jordon‐Thaden, Ingrid E.; Smet, Riet De; Barbazuk, W. Brad; Soltis, Douglas E.; Soltis, Pamela S.

doi:10.3732/apps.1400115

Cited by 125 publications

(153 citation statements)

References 26 publications

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“…MarkerMiner then performs reciprocal BLAST analyses between the latter putative ortholog pairs and a set of user‐specified LSCN gene references ( Oryza and Xerophyta in our case) as a final filter to only retain putative ortholog pairs with putative low‐ to single‐copy status. MarkerMiner only reports the top scoring transcripts from the latter BLAST analyses as putatively orthologous LSCN genes; if additional hits are obtained, these are reported as “secondary transcripts” that may represent splice isoforms, putative paralogs, or partially assembled transcripts, all of which we did not consider for bait design (see Chamala et al., for a complete algorithm). We added Xerophyta as a reference taxon in MarkerMiner, using procedures outlined in Johnson () to create relevant reference files, one containing nucleotide sequences for all genes with introns masked as Ns, and another containing their translation into amino acids.…”

Section: Methodsmentioning

confidence: 99%

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

Gomez

Pokorny

Kantar³

et al. 2019

Appl Plant Sci

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Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea , an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low‐ to single‐copy nuclear genes targeted to work in Dioscorea , assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent‐based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. Results The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm‐wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. Discussion Our customized panel reliably retrieves targeted loci from Dioscorea , is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.

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Section: Methodsmentioning

confidence: 99%

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

Gomez

Pokorny

Kantar³

et al. 2019

Appl Plant Sci

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“…One disadvantage of the transcriptome‐only approach to probe design is that probes spanning intron boundaries will not be effective during sequence capture. Identification of intron‐exon boundaries is possible using MarkerMiner (Chamala et al., ), which aligns transcriptome data to reference genome sequences and returns intron‐masked multiple‐sequence alignments. If no reference genome is available, a low‐coverage genome sequence (10–15× coverage) can also be used to design probes around intron boundaries (Gardner et al., ).…”

Section: Target Enrichmentmentioning

confidence: 99%

Practical considerations for plant phylogenomics

et al. 2018

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The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project‐dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up‐and‐coming technologies that may help propel the field even further.

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“…) and putative single‐copy loci from plant transcriptomes ( markerminer , Chamala et al . ). The challenge of developing new phylogenetic markers lies both in the discovery of conserved regions, the design of primer pairs and an estimation of the level of their phylogenetic signal.…”

Section: Introductionmentioning

confidence: 97%

discomark: nuclear marker discovery from orthologous sequences using draft genome data

Rutschmann

Detering

Simon

et al. 2016

Molecular Ecology Resources

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High‐throughput sequencing has laid the foundation for fast and cost‐effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole‐genome (or whole‐transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well‐supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome‐scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.

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

Cited by 125 publications

References 26 publications

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

Practical considerations for plant phylogenomics

discomark: nuclear marker discovery from orthologous sequences using draft genome data

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