Development of Novel, Exon-Primed Intron-Crossing (EPIC) Markers from EST Databases and Evaluation of their Phylogenetic Utility in <i>Commiphora</i> (Burseraceae)

Premise of the study: Novel nuclear exon-primed intron-crossing (EPIC) markers were developed to increase phylogenetic resolution among recently diverged lineages in the frankincense and myrrh family, Burseraceae, using Citrus, Arabidopsis, and Oryza genome resources. Methods and Results: Primer pairs for 48 nuclear introns were developed using the genome resource IntrEST and were screened using species of Commiphora and other Burseraceae taxa. Four putative intron regions (RPT6A, BXL2, mtATP Synthase D, and Rab6) sequenced successfully for multiple taxa and recovered phylogenies consistent with those of existing studies. In some cases, these regions yielded informative sequence variation on par with that of the nuclear ribosomal DNA internal transcribed spacer. Conclusions: The combination of freely available genome resources and our design criteria have uncovered four single-copy nuclear intron regions that are useful for phylogenetic reconstruction of Burseraceae taxa. Because our EPIC primers also amplify Arabidopsis, we recommend their trial in other rosid and eudicot lineages

Development of novel, Exon-Primed Intron-Crossing (EPIC) markers from EST databases and evaluation of their phylogenetic utility in Commiphora (Burseraceae)

Premise of the study: Novel nuclear exon-primed intron-crossing (EPIC) markers were developed to increase phylogenetic resolution among recently diverged lineages in the frankincense and myrrh family, Burseraceae, using Citrus, Arabidopsis, and Oryza genome resources. Methods and Results: Primer pairs for 48 nuclear introns were developed using the genome resource IntrEST and were screened using species of Commiphora and other Burseraceae taxa. Four putative intron regions (RPT6A, BXL2, mtATP Synthase D, and Rab6) sequenced successfully for multiple taxa and recovered phylogenies consistent with those of existing studies. In some cases, these regions yielded informative sequence variation on par with that of the nrDNA internal transcribed spacer. Conclusions: The combination of freely available genome resources and our design criteria have uncovered four, single-copy nuclear intron regions that are useful for phylogenetic reconstruction of Burseraceae taxa. Because our EPIC primers also amplify Arabidopsis, we recommend their trial in other rosid and eudicot lineages

Plant DNA Barcodes, Community Ecology, and Species Interactions

The community of biologists has been eager to realize the promise of DNA barcodes since the concept of a rapid method for genetic identification of species was first proposed in 2003 [...

Plant DNA Barcodes, Community Ecology, and Species Interactions

The community of biologists has been eager to realize the promise of DNA barcodes since the concept of a rapid method for genetic identification of species was first proposed in 2003 [...

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role

FIGURE 1 in The spiraling story of Tyleropappus and a new name for Calea (Asteraceae: Neurolaeneae) from Venezuela

FIGURE 1. Calea spiralis nom. nov. (Neurolaeneae, Asteraceae). A. Flowering branch. B. Leaf abaxial surface. C. Indumentum of abaxial leaf surface. D. Capitulum. E. First series of phyllaries. F. Second series of phyllaries. G. Third series of phyllaries. H. Fourth series of phyllaries. I. Disc floret with bilength pappus scales. J. Cypsela with polylength pappus scales. A–J drawn from the lectotype H.H. Tate 605 (NY); A–J: millimeter scale. Illustration by Débora Dalzotto.Published as part of &lt;i&gt;Bueno, Vinicius R., Gostel, Morgan R. &amp; Heiden, Gustavo, 2023, The spiraling story of Tyleropappus and a new name for Calea (Asteraceae: Neurolaeneae) from Venezuela, pp. 75-84 in Phytotaxa 622 (1)&lt;/i&gt; on page 78, DOI: 10.11646/phytotaxa.622.1.5, &lt;a href="http://zenodo.org/record/10146668"&gt;http://zenodo.org/record/10146668&lt;/a&gt

FIGURE 2 in The spiraling story of Tyleropappus and a new name for Calea (Asteraceae: Neurolaeneae) from Venezuela

FIGURE 2. Distribution of Calea spiralis nom. nov. (Neurolaeneae, Asteraceae) in Venezuela. VE – Venezuela, BR – Brazil, CO – Colombia.Published as part of &lt;i&gt;Bueno, Vinicius R., Gostel, Morgan R. &amp; Heiden, Gustavo, 2023, The spiraling story of Tyleropappus and a new name for Calea (Asteraceae: Neurolaeneae) from Venezuela, pp. 75-84 in Phytotaxa 622 (1)&lt;/i&gt; on page 79, DOI: 10.11646/phytotaxa.622.1.5, &lt;a href="http://zenodo.org/record/10146668"&gt;http://zenodo.org/record/10146668&lt;/a&gt

Com_mtATPSynthDIntron_APPS2013_MUSCLE

Multiple sequence alignment produced by MUSCLE v.3.7 for phylogenetic analysis of the mtATPSynthase D Intron