Additional file 1 of Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions
Creators: name: Waldbieser, Geoffrey C.
name: Liu, Shikai
name: Yuan, Zihao
name: Older, Caitlin E.
name: Gao, Dongya
name: Shi, Chenyu
name: Bosworth, Brian G.
name: Li, Ning
name: Bao, Lisui
name: Kirby, Mona A.
name: Jin, Yulin
name: Wood, Monica L.
name: Scheffler, Brian
name: Simpson, Sheron
name: Youngblood, Ramey C.
name: Duke, Mary V.
name: Ballard, Linda
name: Phillippy, Adam
name: Koren, Sergey
name: Liu, Zhanjiang
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Comparison of sequences included in the 29 chromosomes of channel catfish genome sequence assembly Coco_2.0 (blue) and Coco_1.2 (red). Figure S2. Xba element sequences are more conserved within channel catfish than in blue catfish. Xba repeats in blue catfish are more divergent even within a single centromere. Shown here are sequence variations of Xba elements from chromosome 2 of blue catfish. Figure S3. Genome level comparison of Billie_1.0 with AU_DB_2.0. Sequence of Wang et al. are on the Y-axis, plotted against Billie_1.0 on the X-axis. Note the potential mis-assemblies by Wang et al., with major artifactual inversions in their assembly indicated within blue oval circles. Figure S4. Chromosomal inversions not reported (chromosome 6, 11, and 24) or created as an assembly artifact (Chromosome 7) from Wang et al.27. In each of the four chromosomes, the upper panels present dot plot alignments of our assembly Billie_1.0 (X-axis) with the assembly of Wang et al. Blue lines represent forward alignment and red lines represent reverse alignment. The lower panels display the dis-concordance of the assembly of Wang et al. with the genetic linkage map of blue catfish. Supplementary Table S1. Summary of PacBio contiguous long read (CLR) sequencing and Illumina sequencing. Supplementary Table S2. Optical map and hybrid assembly. Supplementary Table S3. Comparison of the assemblies of channel catfish and blue catfish reference genomes. Supplementary Table S4. Summary of structural variations between channel catfish genome and blue catfish genome. Supplementary Table S5. Summary of structural variations (SV) greater than 1Mb between channel catfish genome and blue catfish genome. Supplementary Table S6. Gene contents in the inversional segments. Supplementary Table S8. Numbers of genes on each of the 29 chromosomes of channel catfish and blue catfish. Supplementary Table S9. Comparison of annotated protein coding genes from selected teleost species. Channel catfish and blue catfish are highlighted. Supplementary Table S13. Categories of repetitive elements in the blue catfish (Ictalurus furcatus) genome. Supplementary Table S14. Categories of repetitive elements in the channel catfish (Ictalurus punctatus) genome. Supplementary Table S15. Centromere positions in Blue and Channel Catfish chromosomes measured as span of Xba elements. Supplementary Table S16. Centromeric and telomeric sequences for channel and blue catfish chromosome assemblies. Position numbers in red are highlighted as different between channel and blue. Supplementary Table S17. Primers and expected amplicons of junction PCR.