Abstract
Comparative chromosome maps investigating sex chromosomal linkage groups in amniotes and microsatellite repeat motifs of a male house gecko lizard (Hemidactylus frenatus, HFR) and a flat-tailed house gecko lizard (H. platyurus, HPL) of unknown sex were examined using 75 bacterial artificial chromosomes (BACs) from chicken and zebra finch genomes. No massive accumulations of microsatellite repeat motifs were found in either of the gecko lizards, but 10 out of 13 BACs mapped on HPL chromosomes were associated with other amniote sex chromosomes. Hybridization of the same BACs onto multiple different chromosome pairs suggested transitions to sex chromosomes across amniotes. No BAC hybridization signals were found on HFR chromosomes. However, HFR diverged from HPL about 30 million years ago, possibly due to intrachromosomal rearrangements occurring in the HFR lineage. By contrast, heterochromatin likely reshuffled patterns between HPL and HFR, as observed from C-positive heterochromatin distribution. Six out of ten BACs showed partial homology with squamate reptile chromosome 2 (SR2) and snake Z and/or W sex chromosomes. The gecko lizard showed shared unrelated sex chromosomal linkages—the remnants of a super-sex chromosome. A large ancestral super-sex chromosome showed a correlation between SR2 and snake W sex chromosomes.
Highlights
The number of de novo genome sequence assemblies is increasing, in amniote lineages, due to advanced technologies that generate high-quality long reads, greater read depths, and eventual assemblies with fewer and longer contigs per genome [1]
Results showed that only 6.5% of the bacterial artificial chromosomes (BACs) provided identifiable signals attributable to the evolutionary distance between chicken or zebra finch and Gekkonidae of approximately 320 million years ago (MYA) [17,93], while we achieved a 23.5% success rate mapping chicken/zebra finch BACs in snakes [8,10], and 13.0% in Iguanidae [9], which diverged from chicken 90 and 125 MYA, respectively [93] (Table S1)
Current evidence suggests that gecko lizards retain the remnants of unrelated shared sex chromosomal linkages from amniotes
Summary
The number of de novo genome sequence assemblies (reference genomes) is increasing, in amniote lineages, due to advanced technologies that generate high-quality long reads, greater read depths, and eventual assemblies with fewer and longer contigs per genome [1]. The ability to assemble a genome with the same number of contigs as chromosomes (‘chromosome level’ assembly) remains the goal of de novo sequencing. There is little next-generation sequencing data for a large number of species. There have been significant advances in novel techniques such as optical mapping (i.e., BioNano), long-read sequencing (PacBio and Oxford Nanopore Technologies (ONT)), Hi-C linkage mapping (Dovetail), and pre-existing chromosome-level reference assemblies [5,6,7]. It is necessary to integrate technologies for whole-sequence data with molecular cytogenetics in so-called ‘chromosomics’ [14]
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