DOI: 10.5061/dryad.3tx95x6k0
title: Data for: New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog, X. borealis

description: In many groups, sex chromosomes change frequently but the drivers of their
 rapid evolution are varied and often poorly characterized. With an aim of
 further understanding sex chromosome turnover, we investigated the
 polymorphic sex chromosomes of the Marsabit clawed frog, Xenopus borealis,
 using genomic data and a new chromosome-scale genome assembly. We
 confirmed previous findings that 54.1 Mb of chromosome 8L is sex-linked in
 animals from east Kenya and a lab strain, but most (or all) of this region
 is not sex-linked in natural populations from west Kenya. Previous work
 suggests possible degeneration of the Z chromosomes in the east population
 because many sex-linked transcripts of this female heterogametic
 population have female-biased expression, and we therefore expected this
 chromosome to not be present in the west population. In contrast, our
 simulations support a model where the sex-linked portion of the Z
 chromosome from the east acquired autosomal segregation in the west, and
 where the W chromosome from the east was lost in the west. These recent
 changes are consistent with the hot potato model, wherein sex chromosome
 turnover is favoured by natural selection if it purges a (minimally)
 degenerate sex-specific sex chromosome, but counterintuitively suggest
 natural selection failed to purge a Z chromosome that has signs of more
 advanced and possibly more ancient regulatory degeneration. These findings
 highlight complex evolutionary dynamics of young, rapidly evolving Xenopus
 sex chromosomes, and set the stage for mechanistic work aimed at
 pinpointing additional sex-determining genes in this group.
description: <strong>A draft genome
 assembly for <em>X.
 borealis</em></strong>
 DNA was extracted from lysed
 blood of a female frog that was obtained from Nasco (Fort Atkinson, WI,
 USA). Short insert Nextera and TruSeq libraries were prepared,
 respectively, by Jessica B. Lyons and by the Functional Genomics
 Laboratory at the University of California Berkeley, and then sequenced on
 the Illumina HiSeq 2500 (NCBI-SRA:SRR18802894–SRR18802896) by the Vincent
 J. Coates Genomics Sequencing Laboratory at the University of California
 Berkeley (VCGSL). Nextera mate pair libraries were prepared and sequenced
 on the Illumina HiSeq 2500 (NCBI-SRA:SRR18802888 and SRR18802889) by the
 HudsonAlpha Institute for Biotechnology. A Chicago <em>in
 vitro</em> proximity ligation library was prepared by Dovetail
 Genomics and sequenced on the Illumina HiSeq 2500 (NCBI-SRA:SRR18802892
 and SRR18802893) by the VCGSL. Using a liver sample from a male frog, also
 from Nasco, a DpnII Hi-C library was prepared by Dovetail Genomics and
 sequenced on the Illumina HiSeq 2500 (NCBI-SRA:SRR18802890 and
 SRR18802891) by the VCGSL. The short insert data were adapter trimmed with
 ea-utils fastq-mcf version 1.04.807-18-gbd148d4 (Aronesty, 2013). The mate pair data were adapter trimmed and
 split with NxTrim version 0.4.1-53c2193 (O'Connell et al.,
 2015) and filtered using
 nxtrim_pipeline.sh version 1.0 (Bredeson et al., 2021). Trimmed data were then assembled with Meraculous
 version 2.2.4 (Chapman et
 al., 2011). This assembly
 was scaffolded with Chicago and Hi-C data using the Dovetail Genomics
 HiRise algorithm (Putnam
 et al., 2016). 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. Scaffolds smaller than one kb were removed from the final
 assembly with Seqtk version 1.3-r106 (https://github.com/lh3/seqtk). Chromosomes were named according to the corresponding chromosomes in <em>X. tropicalis</em> version 9 (Mitros et al., 2019) and <em>X. laevis</em> version 9 (Session et al., 2016) based on alignment using MUMmer version 4.0.0 (Marcais et al., 2018), and scaffolds were numbered in order of decreasing size using SeqKit version 0.7.2-dev (Shen et al., 2016). The above sequencing reads and draft assembly are deposited under NCBI BioProject PRJNA827809. Assembly statistics were calculated using the Genome Assembly Annotation Service (GAAS) (https://github.com/NBISweden/GAAS). <strong>RRGS data and analysis of sex-linkage</strong> RRGS data from a lab strain and wild-caught individuals were obtained from GenBank, including 49 <em>X. borealis</em> lab strain individuals (PRJNA319044; Furman & Evans, 2016) and 54 <em>X. borealis</em> wild-caught individuals (PRJNA616217; Song et al., 2020). These data were trimmed using Trimmomatic version 0.39 (Bolger et al., 2014), and mapped to the draft <em>X. borealis</em> genome assembly using Bwa version 0.7.17. The HaplotypeCaller, CombineGVCFs, and GenotypeGVCF functions of the Genome Analysis Toolkit (GATK) version 4.1 (McKenna et al., 2010) were used to call genotypes for each sample and combine them into a joint genotype file. The VariantFiltration and SelectVariants functions of GATK were used to filter low-quality genotypes. Positions with the following attributes were removed: QD &gt; 2.0, QUAL &lt; 20, SOR &gt; 3.0, FS &gt; 60.0, MQ &lt; 30.0, where these acronyms respectively refer to variant confidence/quality by depth (QD), genotype quality (QUAL), Symmetric Odds Ratio of 2x2 contingency table to detect strand bias (SOR), Fisher exact test for strand bias (FS), and map quality (MQ). PLINK version 1.9 (Purcell et al., 2007) was used to assess sex-linkage of single nucleotide polymorphisms (SNPs) from the RRGS data that mapped to any of the 18 chromosome assemblies; data from unplaced scaffolds were excluded. <strong>New whole genome sequencing (WGS) data from geographic isolates</strong> New genomic data were generated from a male and female <em>X. borealis</em> individual from east Kenya (field identification numbers BJE4536 and BJE4515, respectively, both from Wundanyi, Kenya) and a male and female individual from west Kenya (BJE4442 and BJE4441, respectively, both from Lukhome, Kenya). Specimens and genetic samples for these individuals are deposited at the Museum of Comparative Zoology at Harvard University, USA (MCZ Herpetology A-153183, MCZ  Herpetology A-153181, MCZ  Herpetology A-153148, MCZ Herpetology A-153147, respectively). These data have been deposited in the NCBI-SRA (BioProject PRJNA616217). The new genomic data were obtained using PCR-free library prep and sequencing each on 1/6th of a lane of a Novaseq S4 machine with paired-end 150 base pair reads. We analyzed these new data along with published genomic data from a female and male individual from our lab strain (BioProject PRJNA421481). We mapped these genomic data to the draft <em>X. borealis</em> genome and called genotypes using the same procedures detailed above for the RRGS data, except that a de-duplication step was performed for the genomic data using Picard (Development_team, 2019) before genotyping. Coverage of the six individuals ranged from 30–46X.
description: Please see manuscript.