A Multi-Tissue Transcriptomic Resource for the Brahminy Blindsnake Indotyphlops braminus (Squamata: Typhlopidae)

The Brahminy blindsnake (Indotyphlops braminus), an all-female, parthenogenetic, and triploid snake, is an informative species for studying polyploidy and asexual reproduction in vertebrates. In this study, we analyzed tissue expression patterns in I. braminus using a PacBio-derived transcript reference and Illumina RNA-seq. Differential expression and annotation over-representation analyses were used to characterize tissue-associated expression differences and over-represented annotations across ovary, heart, liver, and skin from the same three individuals. The three overlapping eye-spot pools were described at the library level. Weighted gene co-expression network analysis (WGCNA) was used only as an exploratory analysis of the 12 four-tissue libraries. A total of 835,353,682 clean read pairs were retained, and gene expression profiles showed broad differences among the four formally analyzed tissues. Of 30,224 tested genes, 13,849 showed a tissue effect, and 4228 candidate tissue-enriched genes were identified by requiring higher expression in all three relevant pairwise comparisons. Six representative annotation terms remained significant in the sensitivity analysis, and 3 of 11 non-gray co-expression modules passed the prespecified stability rule across nine alternative networks. This study provides an additional multi-tissue transcriptomic resource for I. braminus, with candidate sets that can guide future functional and comparative tests of hypotheses concerning parthenogenesis, triploidy, fossoriality, and visual reduction.