Supplementary_Tables_Scheben_et_al_2020

These supplementary tables are data associated with the preprint:

Armin Scheben, Olivia Mendivil Ramos, Melissa Kramer, Sara Goodwin, Sara Oppenheim, Daniel Becker, Michael C Schatz, Nancy B Simmons, Adam Siepel, W Richard McCombie. 2020. Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesomericanus. bioRxiv.

Table legends

Table S4. Recent accumulations of transposable elements identified by RepeatMasker in six noctilionid reference genomes. Base pairs counted are from non-overlapping elements with <6.6% divergence from the consensus sequence as determined by Kimura 2-Parameter corrected rate calculated by calcDivergenceFromAlign.pl.

Table S5. Number of confident (<1e-5) unique blastx alignments of putatative endogenous viral elements to viral families in four noctiolionid bat genomes

Table S6. Number of confident (<1e-5) unique blastx alignments of putatative endogenous viral elements to viral genera in four noctiolionid bat genomes

Table S7. BLASTX alignment results (<1e-5) for putative non-retroviral endogenous viral elements of four noctilionid bats

Table S8. BLASTX alignment results (<1e-5) for putative retroviral endogenous viral elements of four noctilionid bats

Table S9. Table S9. Positively selected genes in the bat ancestor. Raw and within-gene FDR-corrected p-values are provided for the HyPhy aBS-REL test as well as the likelihood ratio test for PAML Test 2 and the null hypothesis Test 2 fixed. Two phylogenetic trees are used, with alternative relationships between laurasiatherian mammals: Tree 1 (Chiroptera + Perissodactyla are sister to the Carnivora + Cetartiodactyla) and Tree 2 (bats as the sister group to a the clade (Cetartiodactyla+Perissodactyla) + Carnivora). Functional groups are defined based on GO annotations for the categories immunity, DNA repair, telomere maintenance, aging, reproduction, thermoregulation, hearing and digestion; genes not belonging to these categories are classified as NA.