Abstract
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.
Highlights
480 complete chloroplast genome sequences are currently publicly available, the majority of which are derived from economically important crop plants
We investigated the differences between the Asian and American E. arvense whole cp genomes
Comparison of the Asian and American E. arvense cp genomes indicated that the Asian E. arvense cp genome large single-copy (LSC) region was 581 bp shorter, the inverted repeats (IRs) region 5 bp shorter, and the small single-copy (SSC) region 8 bp longer than in the American E. arvense cp genome (Table 2)
Summary
480 complete chloroplast (cp) genome sequences are currently publicly available (http://www.ncbi.nlm.nih.gov/ genome), the majority of which are derived from economically important crop plants. Comparative analysis of chloroplast sequences indicate that genome structure, gene content, and gene order are largely stable in land plant lineages [1]. Highly rearranged cp genome structures are observed in some land plant lineages, and can be used as molecular markers to elucidate the ancient divergence of specific groups [2,3,4]. Cp genome comparative analyses were performed using sequences from seed plants in closely related taxa [7,8,9]. Comparison of intraspecific variation in rare and widespread pines indicated low levels of divergence [8]. These data improved our understanding of cp genome evolution and divergence times of closely related taxa. Recent advances in rapid pyrosequencing techniques provide further opportunities to study population diversification and evolution using large numbers of whole cp genome sequences
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