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Viper Genome Aids in Refining Aspects of Snakes' Evolutionary History

NEW YORK (GenomeWeb) – A team from China, Denmark, and the US used a combination of sequencing and comparative genomics to uncover features in snake genomes that may coincide with the evolution of limb loss, venom production, and sensory abilities — work described in Nature Communications.

The researchers generated a high-quality genome assembly for the five-pacer viper (Deinagkistrodon acutus) and compared it to sequences from other snakes, reptiles, and non-reptiles. The comparison gave them insights into subtle shifts in genes, regulatory elements, and genome architecture that mark the snake lineage. For example, along with relaxed selection on developmental genes related to body shape in snakes in general, they found enhanced copy numbers for some venom-related genes that were specific to the five-pacer viper.

"These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution," the authors wrote.

The researchers used the Illumina HiSeq 2000 to do separate paired-end sequencing on genomic DNA from male and female five-pacer vipers, generating around 170 billion bases of sequence data for the male snake and more than 350 billion bases of female snake sequence data. They also sequenced RNA from brain, liver, venom gland, and gonad samples of D. acutus snakes of both sexes.

After putting together a 1.47 billion base draft genome assembly from the male D. acutus reads, the team joined these contigs with higher-coverage female sequences. The resulting genome contained almost 21,200 predicted protein-coding genes, more than 80 percent of which were expressed in at least one of the five-pacer viper tissues considered.

To unravel the five-pacer viper's evolutionary relationships, the researchers compared the new genome with sequences from three other snake species — the Boa constrictor, Python bivittatus, and Ophiophagus hannah — along with genome sequences representing other reptiles such as the green anole lizard. They also included sequences from humans, mice, and other non-reptiles in the phylogenetic analysis.

Based on its phylogenetic tree, the team suggested that the lineage leading to advanced venom-producing snakes such as vipers and cobras split from other snakes roughly 47 million to 84 million years ago, followed by divergence of the viper-king cobra lineages around 28 million to 65 million years ago.

The researchers saw differences in everything from transposable element expansions to sex chromosome differentiation, recombination, and degeneration patterns when they scanned across the snake lineages. Their analyses also offered a look at gene family expansions, contractions, and signatures of selection that occurred within specific snake lineages or across snake species, including changes expected to enhance scent detection, diminish visual acuity, stretch out snake bodies, and mute limb development.

"[T]he newly identified genes under positive selection or under relaxed selective constraint throughout the snake phylogeny in this work can provide informative clues for future experimental work to use the snake as an emerging 'evo-devo' model to understand the genomic architecture of the developmental regulatory networks of organogenesis, or the crosstalk between these networks," the authors wrote.