Abstract
American elm, Ulmus americana L., was widely cultivated in the USA and Canada as a landscape tree. Despite its importance in landscaping and horticulture, its genome is poorly characterized. We assembled the chloroplast genomes of two American elm genotypes (RV16 and Am. 57845); to our knowledge, this is the first description of sequencing and assembly of this species. The complete chloroplast genome of U. americana ranged from 158,935 to 158,993 bp and it contains 127 genes, namely 85 protein-coding genes, 34 tRNA genes, and 8 rRNA genes. Between the two American elm chloroplasts we sequenced, we identified 240 high-quality sequence variants (SNPs and indels). To evaluate the phylogeny of American elm, we compared the chloroplast genomes of the two American elms with seven Asian elm species and twelve other chloroplast genomes available through the NCBI database. As expected, Ulmus was closely related to Morus and Cannabis, as all three genera are assigned to the Urticales. We clarified the timing of the divergence of American elm from the available Asian elms, the divergence within these Asian elms, and all the species’ relative ages. Comparison of the chloroplasts of American elm with the available Asian elms revealed that trnH was absent from American elm but not most Asian elms; conversely, petB, petD, psbL, trnK, and rps16 are present in the American elm but absent from all Asian elms analyzed. ycf15 was present in both American and Asian elms but absent from members of closely related genera. The complete chloroplast genome of U. americana will provide useful genetic resources for characterizing the genetic diversity of U. americana and potentially help to conserve natural populations of American elm.
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Acknowledgments
DNA sequencing was performed at the Purdue University Agricultural Genomics Center, Philip San Miguel, Director.
Author contribution statement
AE: conceived and designed the project, assembled the genomes, analyzed the data, and wrote the original manuscript; JDA: designed portions of the methods, analyzed the data, and revised and edited the final manuscript; CCP, JMS, and CEF: provided leaf samples and edited the draft; KEW: supervised the project and edited and revised the manuscript. All authors contributed to the editing of the final manuscript.
Data archiving statement
The whole chloroplast genome data are deposited as MH324448 and MN043961 in the NCBI database.
Funding
Funding was provided in part by a grant from the Manton Family Trust, the Hardwood Tree Improvement and Regeneration Center (United States Department of Agriculture Forest Service Northern Research Station), and the Department of Forestry and Natural Resources at Purdue University.
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Contribution to the field statement
Genetic diversity within the chloroplast is considered a fundamental tool for understanding population genetic structure and species evolution. We report the assembly and public deposit of the full chloroplast DNA sequences of two genotypes of American elm, and their comparison with Asian elms. These sequences enabled us to identify highly polymorphic regions within the American elm chloroplast that can be used for future studies of genetic diversity, genetic structure, gene flow, hybridization, and genome evolution of American elm.
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Communicated by A.M. Dandekar
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Supplementary information
Supplementary Figure 1
Map of the chloroplast genome of Ulmus americana (Am. 57845). The direction of transcription is indicated by arrows. Genes inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise. Gene function is color-coded as shown in the legend. The darker gray in the inner circle shows the GC content, while the lighter gray shows the AT content. LSC (Large Single Copy region), SSC (Small Single Copy region), IRA, IRB (Inverted Repeat A and B, respectively). The bold black arrow indicates the start position of the chloroplast assembly; the numbering proceeds counter-clockwise. (PNG 5872 kb)
Supplementary Figure 2
Pairwise global nucleotide sequence alignment of Ulmus americana genotypes RV16 and Am. 57845. (PDF 2021 kb)
Supplementary Table 1
The vcf file containing all high-quality variants (SNPs and indels) discovered in the U. americana chloroplast, including functional annotations. (TXT 112 kb)
Supplementary Table 2
The genes in the U. americana chloroplast affected by variants (SNPs and indels). (TXT 3 kb)
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Ebrahimi, A., Antonides, J.D., Pinchot, C.C. et al. The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species. Tree Genetics & Genomes 17, 5 (2021). https://doi.org/10.1007/s11295-020-01487-3
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DOI: https://doi.org/10.1007/s11295-020-01487-3