The genus is globally distributed and comprises approximately 250 species (Troia et al., 2016). ![]() Morphologically, the genus is quite simple and can readily be distinguished from any other group of vascular plants by its narrow leaves containing four air chambers, a single sunken adaxial sporangium covered by a velum and the presence of sporangial trabeculae (Taylor et al., 2016). The genus is the only living survivor of the Isoetales, which arose in the Devonian (Pigg, 1992), and the most ancient species of Isoetes is known from the Late Jurassic (Pigg, 2001). Isoetes is a heterosporous lycophyte that has long fascinated botanists and palaeobotanists alike due to its distinctive morphology and long evolutionary history, which appears to have few parallels among the extant vascular plants (Moran, 2004 Taylor et al., 2009). Phylogenetic inference is being revolutionized with the emergence of next-generation sequencing (NGS), which provides unprecedented opportunities to address fundamental evolutionary questions even for more complex groups that present intriguing evolutionary histories (Soltis et al., 2013), such as the ancient genus Isoetes. Through phylogenetics, we learn not only how species came to be the way they are today but also general principles that enable us to predict how they will change in the future (Yates et al., 2004). It enriches our understanding of how genes, genomes, and species evolve. Recovering the phylogenetic relationships among species is one of the prime goals of systematic and evolutionary biology (Cracraft & Donoghue, 2004). This study will contribute to understanding the diversification of Isoetes and the establishment of a better framework to address the evolutionary history of the genus. In general, genomic traits such as the presence or absence of internal stop codons, a tRNA, and an intron were revealed to be conserved within groups, suggesting that these genomic traits might reveal vital information about the evolution of the genus. Among lycophytes, the gene trnR-CCG was missing only in I. The absence of trnK-UUU was observed in the Brazilian tropical species and in I. Genomic trait mapping analysis showed that the missing introns in the atpF and clpP genes were well conserved in two major clades. andicola was found to be sister to the North American species complex. from Brazil and South Africa into a clade sister to the remaining Isoetes groups. ![]() A basal dichotomy was found that grouped Isoetes spp. The phylogenetic reconstructions detangled the deep relationships in Isoetes and illuminated the more recent radiations in the genus. Our phylogenomic analyses comprising representatives of all major clades yielded well-supported nodes and identical topologies using maximum likelihood and Bayesian inference. Plastomes of six key Isoetes species were annotated, revealing a total of 129 or 130 genes, depending on the species. ![]() The use of next-generation sequencing provides enormous amounts of gene sequences, which allows not only clarification of the basal relationships but also rapid radiations. Although phylogenetic studies have revealed major clades, the deepest relationships in Isoetes remain unresolved.
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