A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.

Data Collection and Assembly. The bat species analyzed in this study and the type of data associated with each are shown in Table 1 . For a few bat species, genomic (chromosomal) sequences are available, and for others, transcriptomic sequences exist. For each bat species with an annotated genome project, we downloaded the relevant RefSeq database from the National Center for Biotechnology Information (NCBI) website and extracted the protein and coding sequence of the longest isoform of each gene for orthology search. After finding orthologous genes from each species, we selected the gene isoform which most closely matched the consensus sequence for further analysis (Methods). Genome assembly accession numbers, as well as basic assembly statistics, for each genome are given in SI Appendix, Table S1 . Human, common shrew (Sorex araneus), and pig (Sus scrofa) genomes were also included as outgroups. Finally, we harvested mRNA and sequenced the transcriptomes of H. monstrosus and R. aegyptiacus on Illumina machines (Methods). For all other bats with available transcriptome data, we downloaded the raw sequencing reads from the Sequence Read Archive (SI Appendix, Table S2 ) (23, (27) (28) (29) (30) (31) (32) (33) (34) (35) (36) (37) (38) .