Genetic variation in the brooding brittle-star: A global hybrid polyploid complex?
Data files
Jan 08, 2025 version files 25.44 GB
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Amphi26_360e0.50dc1_rgsUPGMA.nwk
1.10 MB
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Amphi32b_GTrees.nwk
291.56 KB
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Amphi32b_GTset.txt
4.06 KB
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Amphipholis_16Sv10_mftX.fasta
100.85 KB
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Amphipholis_COI_16S_aln_v2.fasta
66.46 KB
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Amphipholis22MR_200e0.50dc1_rgsUPGMA.nwk
517.60 KB
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Amphipholis32_Trin_across_x5bin_50T_genelist.txt
10 KB
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Amphipholis32_Trin_across_x5bin_50TX.zip
1.91 MB
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MRaligns.zip
614.43 KB
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Raw_read_file_names.csv
1.97 KB
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README.md
3.91 KB
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RHACK.zip
31.17 KB
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SQUAMATA_RAW.zip
25.44 GB
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SRaligns.zip
2.40 MB
Abstract
The widespread and abundant brooding brittle-star (Amphipholis squamata) is a simultaneous hermaphrodite with a complex mitochondrial phylogeography of multiple divergent overlapping mtDNA lineages, high levels of inbreeding or clonality and unusual sperm morphology. We use exon-capture and transcriptome data to show that the nuclear genome comprises multiple (>3) divergent (π > 6%) expressed components occurring across samples characterised by highly divergent (~20%) mitochondrial lineages, and encompassing several other genera, including diploid dioecious species. We report a massive sperm genome size in A. squamata, an order of magnitude larger than that present in other brittlestars, and consistent with our SNP-based measure of greatly elevated ploidy. Similarity of these genetic signatures to well-known animal systems suggests that A. squamata (and related taxa) is a hybrid polyploid asexual complex of variable subgenome origins, ploidy and reproductive mode. We discuss enigmatic aspects of A. squamata biology in this light. This putative allopolyploid complex would be the first to be reported from the phylum Echinodermata.
README: Amphipholis squamata hybrid polyploid swarm data
This dyrad submission contains the DNA next generation Illumina raw reads, aligned nuclear and mitochondrial sequences, and tables of analytical results from our study on the genomic architecture of the brooding brittle star Amphipholis squamata.
Manuscript citation: Hugall, Byrne, OHara (submitted) Brooding brittle-star is a global hybrid polyploid swarm. BioRxiv
Description of the data and file structure
Figure numbers below refer to the submitted paper.
SQUAMATA_RAW: Zipped folder containing the original raw Illumina Next-Gen sequences read files, with table listing the sample identities.
SRalign: Zipped folder containing single read analysis sequence variants, in fasta format. Exon alignment file name follows the structure (project label)_(exon name)_grouprepsCL.fasta. Alignments for 1255 exons. Missing data is coded by tilde (~). Note the number of samples - and sequences per sample, varies between exons. Individual sequence labels comprise sample (genus_species_sample ID), followed by codes for the clustering level (dc# where # is the number of differences allowed in a cluster), a unique identifier for a sample variant at a particular clustering level (grp#), and the total read coverage for that sequence variant (c#).
MRalign: Zipped folder containing the merged read equivalent of SRalign.
RHACK: Zipped folder containing the Bash scripts for the sequence variant read mapping system (RHACK3cp.sh) and attendant accessory files: 1552exons.txt position table of the total ophiouroid exon capture system exons (columns: exon name, length, start position, end position); RevTable.txt for sequence reverse compliment translation. See Hugall et al. (2016) (doi:10.1093/molbev/msv216) for further details on exon capture system, pipeline and target. HETTER2.sh for calculating minor state frequencies (see Figure 5).
Amphipholis_COI_16S_aln_v2.fasta: Mitochondrial COI and 16S alignment used to generate a mitochondrial phylogeny (Figure 3a). Fasta format.
Amphipholis_16Sv10_mftX.fasta: Fasta format alignment of partial mitochondrial 16S from GenBank and our samples, used to generate 16S phylogeny Figure S1. GenBank samples label starts with accession number.
Amphipholis32_Trin_across_x5bin_50TX.zip: Exon capture pipeline sample-specific reference concatenated sequence, trimmed to remove sites where less than 50% of samples have a defined base (ACGT). Fasta format compressed. Used to generate Figure 3b.
Amphipholis32_Trin_across_x5bin_50T_genelist.txt: The matching exon capture partition file for the concatenated exon capture alignment. Format as for the 1552exons.txt list but the exons have been grouped into genes.
Amphi32b_GTrees.nwk: Newick format file of the gene trees made from the individual gene partitions in the concatenated alignment. Gene trees (n=234) used to generate ASTRAL summary tree (Figure S2)
Amphi32b_GTset.txt: Text format table listing the genes used to create the gene trees with four columns: name of gene, number of samples, total number of sites, and number of variable sites.
Amphi26_360e0.50dc1_rgsUPGMA.nwk: P-distance UPGMA trees generated from 360 single read analysis exon sequence variant alignments (SRaligns), using the dc1 clustering level sequences.
Amphipholis22MR_200e0.50dc1_rgsUPGMA.nwk: P-distance UPGMA tree generated from 200 merged read analysis exon sequence variant alignments (MRaligns), using the dc1 clustering level sequences. Figure 2 is an example of one of these trees.
Sharing/Access information
Novel mitochondrial COI and 16S sequences are deposited in NCBI/nucleotide
Previous dryad submission(s) with the exon-capture methodology include
All data is included in this dryad submission
Code/Software
This submission includes some UNIX bash code for analysing the Illumina raw DNA paired end reads, and R code for producing the figures.
Methods
Exon capture next-generation DNA sequence data, including mitochondrial genes
Bioinformatic scripts (R and Bash) and data tables