Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Abstract

Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (HiC) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl configuration similar to the "bouquet" structure of meiotic cells. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog X. borealis

“…The mitochondrial genome was assembled from adapter trimmed data using organelle_pipeline.py version 1.0 (Bredeson et al, 2021) and NOVOPlasty version 2.6.3 (Dierckxsens et al, 2017), starting with other Pipidae mitochondrial assemblies available on NCBI as input seeds. The assembly was screened with general_decon.sh version 1.0 (Mudd et al, 2020) to identify archaea, bacteria, virus and vector contaminants using the respective RefSeq and UniVec databases, queried using mt_decon.sh version 1.0 (Mudd et al, 2020) against the mitochondrial assembled sequence and filtered using nt_decon.sh version 1.0 (Bredeson et al, 2021) against the NT database and other completed frog assemblies. The assembly was then run through align_pipeline.sh version 1.0 (Bredeson et al, 2021) to identify and remove duplicate haplotype sequences.…”

“…The assembly was screened with general_decon.sh version 1.0 (Mudd et al, 2020) to identify archaea, bacteria, virus and vector contaminants using the respective RefSeq and UniVec databases, queried using mt_decon.sh version 1.0 (Mudd et al, 2020) against the mitochondrial assembled sequence and filtered using nt_decon.sh version 1.0 (Bredeson et al, 2021) against the NT database and other completed frog assemblies. The assembly was then run through align_pipeline.sh version 1.0 (Bredeson et al, 2021) to identify and remove duplicate haplotype sequences. Scaffolds smaller than 1 kb were removed from the final assembly with Seqtk version 1.3‐r106 (https://github.com/lh3/seqtk).…”

“…sh version 1.0 (Mudd et al, 2020) against the mitochondrial assembled sequence and filtered using nt_decon.sh version 1.0 (Bredeson et al, 2021) against the NT database and other completed frog assemblies. The assembly was then run through align_pipeline.sh version 1.0 (Bredeson et al, 2021) to identify and remove duplicate haplotype sequences. Scaffolds smaller than 1 kb were removed from the final assembly with Seqtk version 1.3-r106 (https://github.…”

Molecular conflicts disrupting centromere assembly contribute to Xenopus hybrid inviability

“…X. laevis and X. tropicalis CENP-A CHIP-seq datasets were used from previously described studies (Smith et al, 2021; Bredeson et al, 2021). CENP-A ChIP and Input libraries from each species were processed to identify CENP-A enriched k -mers using the k -mer counting pipeline that normalizes k -mer counts by sequencing depth of each library (https://github.com/straightlab/xenla-cen-dna-paper).…”

Molecular conflicts disrupting centromere maintenance contribute to Xenopus hybrid inviability

“…laevis and X. tropicalis CENP-A CHIP-seq datasets were used from previously described studies. 26,72 CENP-A ChIP and Input libraries from each species were processed to identify CENP-A enriched k-mers using the k-mer counting pipeline that normalizes k-mer counts by sequencing depth of each library (https://github.com/straightlab/xenla-cen-dna-paper). For this study 25bp k-mers were used and kmc was run with ci=10, indicating that k-mers must be found 10 times in the dataset to be considered.…”