Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes
Lee, Ling Sze
Navarro-Domínguez, Beatriz M.
Montiel, Eugenia E.
Gessler, Thea B.
© 2020 by the authors
Is Version Of
Ecology, Evolution and Organismal Biology
Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use optical mapping to improve the contiguity of the painted turtle (Chrysemys picta) genome assembly and use de novo fluorescent in situ hybridization (FISH) of bacterial artificial chromosome (BAC) clones, BAC-FISH, to physically map the genomes of the painted and slider turtles (Trachemys scripta elegans). Optical mapping increased C. picta’s N50 by ~242% compared to the previous assembly. Physical mapping permitted anchoring ~45% of the genome assembly, spanning 5544 genes (including 20 genes related to the sex determination network of turtles and vertebrates). BAC-FISH data revealed assembly errors in C. picta and T. s. elegans assemblies, highlighting the importance of molecular cytogenetic data to complement bioinformatic approaches. We also compared C. picta’s anchored scaffolds to the genomes of other chelonians, chicken, lizards, and snake. Results revealed a mostly one-to-one correspondence between chromosomes of painted and slider turtles, and high homology among large syntenic blocks shared with other turtles and sauropsids. Yet, numerous chromosomal rearrangements were also evident across chelonians, between turtles and squamates, and between avian and non-avian reptiles.
This aritcle is published as Lee, Ling S., Beatriz M. Navarro-Domínguez, Zhiqiang Wu, Eugenia E. Montiel, Daleen Badenhorst, Basanta Bista, Thea B. Gessler, and Nicole Valenzuela. 2020. "Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes" Genes 11, no. 8: 928. https://doi.org/10.3390/genes11080928. Posted with permission. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
physical molecular cytogenetic BAC clone mapping, genome and chromosome evolution, BioNano optical genome mapping, avian, squamate, and chelonian vertebrates, turtle, lizard and snake non-avian reptiles, genome alignments, Chrysemys picta and Trachemys scripta, karyotype evolution, phylogenomics