Low‐coverage, whole‐genome sequencing of <i>Artocarpus camansi</i> (Moraceae) for phylogenetic marker development and gene discovery

Gardner, Elliot M.; Johnson, Matthew G.; Ragone, Diane; Wickett, Norman J.; Zerega, Nyree J. C.

doi:10.3732/apps.1600017

Cited by 43 publications

(68 citation statements)

References 35 publications

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“…S11). A similar pattern of multicopy genes recovered from exon capture data has been reported in Artocarpus (Moraceae; Johnson et al ., ), which is known to have undergone at least one whole genome duplication (Gardner et al ., ). This suggests that the pattern detected in Lachemilla , Alchemilla , and Aphanes might also be the result of an ancient whole genome duplication that predates the diversification of the clade.…”

Section: Discussionmentioning

confidence: 97%

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

2018

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Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.

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Section: Discussionmentioning

confidence: 97%

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

2018

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“…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., ). Finally, the pipeline Sondovač (Schmickl et al., ) uses a combination of transcriptome and genome skimming data to identify possible nuclear exons, and their introns, to be captured.…”

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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“…Sequencing libraries were hybridized to a bait set comprising 458 target nuclear coding regions. We describe the development of bait sequences from a draft genome sequence in a companion paper (Gardner et al, 2016). Briefly, 333 loci intended for phylogenetic analysis were selected by identifying long exons homologous between the Artocarpus draft genome and the published genome of Morus notabilis C. K. Schneid.…”

Section: Methods and Resultsmentioning

confidence: 99%

“…A set of 125 additional genes were targeted for their functional significance: 98 MADS-box genes and 27 genes that have been implicated in floral volatiles. For the genes of functional significance, baits were designed from the A. camansi Blanco draft genome alone (Gardner et al, 2016). A set of 20,000 baits (biotinylated RNA oligonucleotides, the smallest MYbaits kit) with 3× tiling was manufactured by MYcroarray (Ann Arbor, Michigan, USA).…”

Section: Methods and Resultsmentioning

confidence: 99%

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HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment

et al. 2016

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Premise of the study:Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).Methods and Results:HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.Conclusions:HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.

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Low‐coverage, whole‐genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery

Cited by 43 publications

References 35 publications

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Practical considerations for plant phylogenomics

HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment

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