Draft genome assemblies and SSR-Seq dataset for Simarouba amara and S. versicolor , native species to Latin America

Abstract

Simarouba amara (known in Brazilian Portuguese as “marupá”) and S. versicolor (known in Brazilian Portuguese as “pé-de-perdiz”) are Neotropical species belonging to the family Simaroubaceae. These species have historically been used in folk medicine to treat conditions such as malaria, cancer, helminthiasis, viral infections, gastritis, ulcers, di- arrhea, and diabetes. Recent advances in high-throughput sequencing (HTS) technologies have improved the acquisi- tion of genomic datasets for economically wild species. This genomics data enables the development of microsatellite markers (SSR), which are valuable tools in genetic analy- sis, mainly in species with absence of genomic resources, as S. amara and S. versicolor . In this study, we generated high-quality draft assemblies and developed SSR-Seq primers from these assemblies, for both species. We sequenced a total of 20,273,467 and 16,800,708 reads from S. amara and S. versicolor , respectively, with an estimated genome sizes of 372.16 Mb and 249.78 Mb. The genome assemblies by SPAdes resulted in 23,601 and 23,722 total contigs and an N50 value of 28,440 bp and 22,312 bp. Using the QDD pipeline, we identified 11,348 and 12,084 microsatellite regions that are putative for primers design. Using the openPrimeR tool, this dataset was filtered and 87 and 77 sets of SSR-Seq primers survived. Using physicochemical properties, 55 and 56 SSR-seq primer pairs for S. amara and S. versicolor were organized into five and four multiplex sets. The SSR-Seq dataset developed in this study enables the acquisition of genetic information and performs genetic and evolutionary analyses in these wild populations.