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Comparative analyses of complete chloroplast (cp) DNA sequences within a species may provide clues to understand the population dynamics and colonization histories of plant species.  Equisetum arvense  (Equisetaceae) is a widely distributed fern species in northeastern Asia, Europe, and North America. The complete cp DNA sequences from Asian and American  E. arvense  individuals were compared in this study. The Asian  E. arvense  cp genome was 583 bp shorter than that of the American  E. arvense . In total, 159 indels were observed between two individuals, most of which were concentrated on the hypervariable  trnY-trnE  intergenic spacer (IGS) in the large single-copy (LSC) region of the cp genome. This IGS region held a series of 19 bp repeating units. The numbers of the 19 bp repeat unit were responsible for 78% of the total length difference between the two cp genomes. Furthermore, only other closely related species of  Equisetum  also show the hypervariable nature of the  trnY-trnE  IGS. By contrast, only a single indel was observed in the gene coding regions: the  ycf1  gene showed 24 bp differences between the two continental individuals due to a single tandem-repeat indel. A total of 165 single-nucleotide polymorphisms (SNPs) were recorded between the two cp genomes. Of these, 52 SNPs (31.5%) were distributed in coding regions, 13 SNPs (7.9%) were in introns, and 100 SNPs (60.6%) were in intergenic spacers (IGS). The overall difference between the Asian and American  E. arvense  cp genomes was 0.12%. Despite the relatively high genetic diversity between Asian and American  E. arvense , the two populations are recognized as a single species based on their high morphological similarity. This indicated that the two regional populations have been in morphological stasis.

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Chloroplast Genome Differences between Asian and American Equisetum arvense (Equisetaceae) and the Origin of the Hypervariable trnY-trnE Intergenic Spacer