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.; Wu, Zhiqiang; Montiel, Eugenia E.; Badenhorst, Daleen; Bista, Basanta; Gessler, Thea B.; Valenzuela, Nicole

doi:10.3390/genes11080928

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Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes

Ling Sze Lee

^†

Beatriz M. Navarro-Domínguez

^†,‡,

^§

^‖,

and

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA

Author to whom correspondence should be addressed.

^†

Contributed equally as first authors.

^‡

Current address: Department of Biology, University of Rochester, Rochester, NY 14627, USA.

^§

Current address: Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China.

^‖

Current address: Departamento de Biología Experimental, Universidad de Jaén, 23071 Jaén, Spain.

Genes 2020, 11(8), 928; https://doi.org/10.3390/genes11080928

Received: 8 July 2020 / Revised: 25 July 2020 / Accepted: 31 July 2020 / Published: 12 August 2020

(This article belongs to the Special Issue Vertebrate Karyotype Evolution: How Far Have We Come, and Where Are We Going?)

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Abstract

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. View Full-Text

Keywords: 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

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Lee, L.S.; Navarro-Domínguez, B.M.; Wu, Z.; Montiel, E.E.; Badenhorst, D.; Bista, B.; Gessler, T.B.; Valenzuela, N. Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes. Genes 2020, 11, 928. https://doi.org/10.3390/genes11080928

AMA Style

Lee LS, Navarro-Domínguez BM, Wu Z, Montiel EE, Badenhorst D, Bista B, Gessler TB, Valenzuela N. Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes. Genes. 2020; 11(8):928. https://doi.org/10.3390/genes11080928

Chicago/Turabian Style

Lee, Ling Sze, 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

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Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes

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