Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly

• Published in: Genome biology and evolution Vol. 16; no. 3
• Main Authors: Webster, Timothy H, Vannan, Annika, Pinto, Brendan J, Denbrock, Grant, Morales, Matheo, Dolby, Greer A, Fiddes, Ian T, DeNardo, Dale F, Wilson, Melissa A
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 02.03.2024
• Subjects: Animals; Animals, Poisonous; Dosage compensation; Dosage Compensation, Genetic; Female; Females; Genomes; Genomics; Heloderma suspectum; Karyotype; Karyotypes; Lizards - genetics; Male; Males; Sex chromosomes; Sex Chromosomes - genetics; Sex determination; Somatic chromosomes; Transcriptomes; Whole genome sequencing; Z chromosomes; expression; Anguimorpha; sex chromosome evolution; reptiles; squamate; ZW system; genome assembly
• ISSN: 1759-6653; 1759-6653
• DOI: 10.1093/gbe/evae018

Abstract Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates. Graphical Abstract