Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard
Links
- More information: Publisher Index Page (via DOI)
- Open Access Version: Publisher Index Page
- Download citation as: RIS | Dublin Core
Abstract
Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334–127 Mb) representing macrochromosomes and 8 small scaffolds (63–22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.
| Publication type | Article |
|---|---|
| Publication Subtype | Journal Article |
| Title | Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard |
| Series title | Genome Biology and Evolution |
| DOI | 10.1093/gbe/evad210 |
| Volume | 15 |
| Issue | 12 |
| Year Published | 2023 |
| Language | English |
| Publisher | Oxford Academic |
| Contributing office(s) | Western Ecological Research Center |
| Description | evad210, 14 p. |
| Google Analytic Metrics | Metrics page |