Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python)

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(a) Multiple sequence alignment of epididymal protein E1. Twenty species representing fish, parasite, insect, snake, turtle, lizard, alligator, chicken, mouse, cow, horse, dog, cat, chimpanzee, and human conserved regions of the alignment are indicated in blue while nonconserved regions are shown in red. Sequences from the snake species Opheodrys aestivus, Pantherophis guttatus, Echis coloratus, Python regius, and Python bivittatus all contain a 5-amino-acid insertion (KRGEM in python species) within the first ten amino acids of the alignment in comparison to other reptiles and mammalian species. Similarly, the primate lineage, represented by Homo sapiens and Pan troglodytes, exhibits a 2-amino-acid insertion (HL) at the very end of the alignment. Thelohanellus kitauei (an aquatic invertebrate parasite) and Bombus impatiens (bee) provide evidence for an ancient role of this gene in the common ancestor of insects, parasites, and vertebrates. (b) Phylogenetic tree of epididymal protein E1. The multiple sequence alignment shown in Figure 3(a) was used to generate a phylogenetic tree using a bootstrapping approach. The number near each root or interior node of the tree indicates how many times the same subtree, as shown in the image, was obtained when the input sequences were sampled during the bootstrapping. In this tree, Python regius and Python bivittatus are grouped together in all 10,000 trees produced during the phylogenetic tree construction process. Similarly, the Homo sapiens and Pan troglodytes subtree also exhibits a count of 10000. The scale bar below the tree provides an estimate for sequence evolution rate between the taxa. (c) Multiple sequence alignment of mitochondrial cytochrome b protein. The cytochrome b protein was aligned across multiple species to visualize the sequence relationship between Python regius and Python bivittatus in the context of other species. Conserved regions of the alignment are indicated in blue while less conserved regions are shown in red. The species representing snakes exhibit an absence of the 5 amino acids within the first ten amino acids of the alignment. This sequence feature is not observed in other reptiles, Gallus gallus (chicken) and Oncorhynchus mykiss (trout), or in mammals. Thus, there is the possibility that certain aspects of biology and/or physiology may be uniquely shared among snakes.

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