Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms

Here we briefly describe the provided files. Transcriptomics were performed on 12 Coelaturini, which are indicated in Supplementary Table 1 of Ortiz-Sepulveda et al. (2022). Enrichment of ORF and UCE targets from genomic DNA libraries of 96 individuals, i.e. 95 Coelaturini and one iridinid bivalve, which are outlined in Supplementary Table 3 of Ortiz-Sepulveda et al. (2022). Specifically, 48 individuals were included for phylogenetic analysis at a continental scale and 48 specimens of Coelaturini from the Malawi Basin were included for population genomics.

Bioinformatic scripts are available via www.github.com/bertvanbocxlaer/target_enrichment_ORF_UCE. Raw sequencing data are available at NCBI under BioProject PRJNA893605. BioSamples SAMN31437443-SAMN31437454 contain raw sequencing reads from RNA-seq, whereas raw sequencing reads from target enrichment are available under SAMN31439307-SAMN31439402. Below is information on each file uploaded to Dryad:

Ortiz-Sepulveda_et_al-CoelaturiniSupertranscriptome_95p_ORFs_95p.fa

This file contains all open reading frames (ORFs) that were considered for our orthology assessment. More precisely, we first clustered our 12 de novo assembled transcriptomes into a supertranscriptome by grouping all contigs with >95% similarity and representing each group by the longest contig. Subsequently, we predicted ORFs on these contigs and selected the best-supported ORF per contig. This pool of ORFs was then clustered again to retain homologous ORF clusters, each of which contains all ORFs with >95% similarity. This resulting library of ORF homologs was then used for comparisons to the BUSCO Metazoa_odb9 database (Simão et al., 2015; Waterhouse et al., 2017) and the Unioverse probe set (Pfeiffer et al., 2019).

Ortiz-Sepulveda_et_al-FinalTargets_ORFs_UCEs.fasta

This file contains the final ORF and UCE targets considered for probe design with a MyBaits custom kit for target enrichment. Each .fasta sequence represents a complete target. Targets that were selected for probe design, but for which no probes could be designed are still present in this file. Specifically, this concerns three UCE targets, i.e. >slice-1603-chr13-pos-2343997-2344108-6-UCE-str, >slice-1421-chr9-pos-9900750-9900854-6-UCE-str and >slice-3362-chr5-pos-36441263-36441395-5-UCE-opt.

Ortiz-Sepulveda_et_al-Additional_Data_Tables.xlsx

This file contains four additional data tables. Additional tables 1 and 2 contain data on specimen representation, alignment length, and the proportion of informative and missing sites for each ORF and UCE locus, respectively. Additional tables 3 and 4 contain the results of the partition analysis using Modeltest in IQTREE for ORFs and UCEs, respectively. For ORFs we obtained a 402–partition scheme with 45 unique substitution models, whereas for UCEs a 155-partition scheme with 51 unique substitution models.

Ortiz-Sepulveda_et_al-Coelaturini_Mitogenome_FINAL.fasta

This file contains the entire female-inherited mitogenome obtained for Coelaturini from the Malawi Basin through iterative rounds of genome skimming.

Ortiz-Sepulveda_et_al-Coelaturini_Mitogenes_FINAL.fasta

This file contains the sequences of the genes of the female-inherited mitogenome of Coelaturini from the Malawi Basin.

Ortiz-Sepulveda_et_al-Mitogenome_annotations_FINAL.gff

This file contains the annotation of the entire female-inherited mitogenome obtained for Coelaturini from the Malawi Basin.

no_SRR_0.99_lognorms-cutoff-no_ref_mafft-clean-50p-concat_trimmed.fasta-out.fas

This file contains the final concatenated alignment of our open reading frames (after all cleaning procedures) as used for phylogenetic reconstruction.

0.99_lognorms-cutoff-mafft-fasta-notrim-clean-50p-concat-trim.fasta
This file contains the final concatenated alignment for our ultraconserved element (after all cleaning procedures) as used for phylogenetic reconstruction.

Capture_ORF_45_filtered_08.vcf.gz

This file contains the final variant calling information for our open reading frames (exons only, without intronic/intergenic flanking regions) that is used as input for Pixy to calculate nucleotide diversity (π), the absolute nucleotide divergence between population pairs (D_XY) and population differentiation (F_ST).

Capture_UCE_45ind_filtered_08.vcf.gz
This file contains the final variant calling information for our ultraconserved elements (with flanking regions) that is used as input for Pixy to calculate nucleotide diversity (π), the absolute nucleotide divergence between population pairs (D_XY) and population differentiation (F_ST).

clean_80_mac3_45_m95_maf_005_8.recode.vcf

This file contains the final variant calling information for our open reading frames (without intronic/intergenic flanking regions) that is used to examine genetic structure with principal component analysis and fastSTRUCTURE.

References 

Pfeiffer, J. M., Breinholt, J. W., & Page, L. M. (2019). Unioverse: a phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida). Molecular Phylogenetics and Evolution, 137, 114-126.

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), 3210-3212.

Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., . . . Zdobnov, E. M. (2017). BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular Biology and Evolution, 35(3), 543-548.

Funding provided by: Agence Nationale de la Recherche
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001665
Award Number: ANR-17-CE02-0015