International Journal of Molecular Sciences Article Plastid Genomes of the Early Vascular Plant Genus Selaginella Have Unusual Direct Repeat Structures and Drastically Reduced Gene Numbers Hyeonah Shim 1, Hyeon Ju Lee 1, Junki Lee 1,2, Hyun-Oh Lee 1,2, Jong-Hwa Kim 3, Tae-Jin Yang 1,* and Nam-Soo Kim 4,* 1 Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea;
[email protected] (H.S.);
[email protected] (H.J.L.);
[email protected] (J.L.);
[email protected] (H.-O.L.) 2 Phyzen Genomics Institute, Seongnam 13558, Korea 3 Department of Horticulture, Kangwon National University, Chuncheon 24341, Korea;
[email protected] 4 Department of Molecular Bioscience, Kangwon National University, Chuncheon 24341, Korea * Correspondence:
[email protected] (T.-J.Y.);
[email protected] (N.-S.K.); Tel.: +82-2-880-4547 (T.-J.Y.); +82-33-250-6472 (N.-S.K.) Abstract: The early vascular plants in the genus Selaginella, which is the sole genus of the Selaginel- laceae family, have an important place in evolutionary history, along with ferns, as such plants are valuable resources for deciphering plant evolution. In this study, we sequenced and assembled the plastid genome (plastome) sequences of two Selaginella tamariscina individuals, as well as Se- laginella stauntoniana and Selaginella involvens. Unlike the inverted repeat (IR) structures typically found in plant plastomes, Selaginella species had direct repeat (DR) structures, which were confirmed by Oxford Nanopore long-read sequence assembly.