Novel SINE2, SINE3, and retro pseudogenes derived from the 5S ribosomal gene in the genome of yaguareté and related Felidae

Description

We conducted a structural search for SINEs in the NCBI reference genomes of twenty-three species of Felidae (cat family). Those species included Acinonyx jubatus (cheetah) (GCF_027475565.1), Caracal caracal (GCA_016801355.1), Felis catus (domestic cat) (GCF_018350175.1), F. chaus (jungle cat) (GCA_019924945.1), F. nigripes (black-footed cat) (GCA_032458615.1), Herpailurus yagouaroundi (jaguarundi) (GCF_014898765.1), Leopardus pardalis albescens (GCA_058742865.1), Leptailurus serval (serval) (GCA_056512435.1), Lynx canadensis (Canada lynx) (GCF_007474595.2), L. pardinus (Iberian lynx) (GCA_900661375.1), L. rufus (bobcat) (GCF_022079265.1), Neofelis diardi (Sunda clouded leopard) (GCA_027422475.1), N. nebulosa (Clouded leopard) (GCF_028018385.1), Otocolobus manul (Pallas's cat) (GCA_028564725.2), Panthera leo (lion) (GCF_018350215.1), P. onca (yaguareté) (GCF_046562875.1), P. pardus (leopard) (GCF_024362965.1), P. tigris (tiger) (GCF_018350195.1), P. uncia (snow leopard) (GCF_023721935.1), Prionailurus bengalensis (leopard cat) (GCF_016509475.1), P. iriomotensis (Iriomote cat) (GCA_054601675.1), P. viverrinus (fishing cat) (GCF_022837055.1), and Puma concolor (puma) (GCF_003327715.1). We found and subsequently characterized five novel SINE retroposons (FelidaeSINE2-1, FelidaeSINE2-2, FelidaeSINE2-3, FelidaeSINE2-4, FelidaeSINE3), the 5S rRNA gene and derived retro pseudogenes (Felidae5SrRNA, Felidae5SRPG1, Felidae5SRPG2, Felidae5SRPG3), and DNA stretches formed by the repetition of SINEs (Repeat_FelidaeSINE2-1X2, Repeat_FelidaeSINE2-1X3, Repeat_FelidaeSINE2-1X4, Repeat_FelidaeSINE2-1X5, Repeat_FelidaeSINE2-1X6, Repeat_FelidaeSINE2-2/FelidaeSINE2-1, Repeat_FelidaeSINE2-3/FelidaeSINE2-1). The constructed consensus sequences include all species, except for Repeat_FelidaeSINE2-1X5 and Repeat_FelidaeSINE2-1X6 which were found in a smaller number of taxa. Here, we provide the associated files and encourage the scientific community to use them.

Institutions

• National University of Misiones

  Misiones, Posadas
• Consejo Nacional de Investigaciones Científicas y Técnicas

  Buenos Aires F.D., Buenos Aires

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