Capture of hemoglobin clusters

Combining high-throughput sequencing with targeted sequence capture has becomean attractive tool to study specific genomic regions of interest. Most studies have so farfocused on the exome using short-read technology. These approaches are not designedto capture intergenic regions needed to reconstruct genomic organization, includingregulatory regions and gene synteny. Here, we demonstrate the power of combiningtargeted sequence capture with long-read sequencing technology for comparativegenomic analyses of the hemoglobin (Hb) gene clusters across eight species separatedby up to 70 million years. Guided by the reference genome assembly of the Atlantic cod(Gadus morhua) together with genome information from draft assemblies of selectedcodfishes, we designed probes covering the two Hb gene clusters. Use of custom-madebarcodes combined with PacBio RSII sequencing led to highly continuous assemblies ofthe LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of codingand intergenic sequences. Our results revealed an overall conserved geneticorganization and synteny of the Hb genes within this lineage, yet with several, lineagespecific gene duplications. Moreover, for some of the species examined, we identifiedamino acid substitutions at two sites in the Hbb1 gene as well as length polymorphismsin its regulatory region, which has previously been linked to temperature adaptation inAtlantic cod populations. This study highlights the use of targeted long-read capture asa versatile approach for comparative genomic studies by generation of a cross-speciesgenomic resource elucidating the evolutionary history of the Hb gene family across thehighly divergent group of codfishes.

160111_Gmorhua_capture_probes.zipSequences of the different probes.Hb_target_region_gadmor2.fasta.gzThe target regions from the gadMor2 genome assembly.brosme_brosme.rawreads.fastq.gzThe raw reads from capture for Brosme brosme.brosme_brosme_hb_assembly.fasta.gzThe assembled hemoglobin regions of Brosme brosme.gadiculus_argenteus.rawreads.fastq.gzThe raw reads from capture for Gadiculus argenteus.gadiculus_argenteus_hb_assembly.fasta.gzThe assembled hemoglobin regions of Gadiculus argenteus.gadus_morhua.rawreads.fastq.gzThe raw reads from capture for Gadus morhua.gadus_morhua_hb_assembly.fasta.gzThe assembled hemoglobin regions of Gadus morhua.lota_lota.rawreads.fastq.gzThe raw reads from capture for Lota lota.lota_lota_hb_assembly.fasta.gzThe assembled hemoglobin regions of Lota lota.macrourus_berglax.rawreads.fastq.gzThe raw reads from capture for Macrourus berglax.macrourus_berglax_hb_assembly.fasta.gzThe assembled hemoglobin regions of Macrourus berglax.melanogrammus_aeglefinus.rawreads.fastq.gzThe raw reads from capture for Melanogrammus aeglefinus.melanogrammus_aeglefinus_hb_assembly.fasta.gzThe assembled hemoglobin regions of Melanogrammus aeglefinus.merluccius_merluccius.rawreads.fastq.gzThe raw reads from capture for Merluccius merluccius.merluccius_merluccius_hb_assembly.fasta.gzThe assembled hemoglobin regions of Merluccius merluccius.muraenolepsis_marmoratus.rawreads.fastq.gzThe raw reads from capture for Muraenolepsis marmoratus.muraenolepsis_marmoratus_hb_assembly.fasta.gzThe assembled hemoglobin regions of Muraenolepsis marmoratus.Boreogadus_saida_fish_2LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Boreogadus_saida_fish_2MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Gadiculus_argentus_fish_8LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Gadiculus_argentus_fish_8MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Lota_lota_fish_11LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Lota_lota_fish_11MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Macrourus_berglax_fish_17LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Macrourus_berglax_fish_17MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Melanogrammus_aeglefinus_fish_5LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Melanogrammus_aeglefinus_fish_5MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Merluccius_merluccius_fish_13LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Merluccius_merluccius_fish_13MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Muraenolepis_marmoratus_fish_20LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Muraenolepis_marmoratus_fish_20MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Theragra_chalcogramma_fish_7LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Theragra_chalcogramma_fish_7MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Trachyrincus_scabrus_fish_36LA_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.Trachyrincus_scabrus_fish_36MN_scf.fasta.gzFrom low-coverage genome assembly, used for probe design.