contigs scaffolded using bionano solve v3.7  (BioNano Genomics)

Journal: bioRxiv

Article Title: Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

doi: 10.1101/2024.10.28.620687

Figure Lengend Snippet: Representative alignments of inversions or double inversions identified from blood samples obtained from 30 individuals from eleven species. For each inversion, the top shows predicted motifs from an in-situ digest of the reference genome, the bottom shows motifs identified using Bionano molecules obtained from an individual of the species indicated on the left, and the grey lines indicate matching motifs based upon predicted and observed distances. Single inversions were identified on chromosomes 2, 9, 10, 13, and 20. Tandem double inversions were identified on chromosomes 11 and 20. The estimated length and percentage of the chromosome spanned by the inversion is shown on the right. The single inversion on 20 identified in Rhamphochromis longiceps has the same position as the first inversion of the double inversion on 20 identified from Mchenga conophoros . A list of all samples and their inversion genotype is in . Note that an error in the reference genome in chromosome 2 is indicated in the first panel.

Article Snippet: These differences fall into two primary categories: 1) contigs that were incorrectly ordered or oriented and 2) unplaced contigs that Bionano anchored to specific chromosomes.

Techniques: In Situ

Journal: bioRxiv

Article Title: Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

doi: 10.1101/2024.10.28.620687

Figure Lengend Snippet: ( A ) Schematic of the two inversion states (normal and inverted) and their assignment as X or Y chromosomes. ( B ) 24 o‘spring (12 male and 12 female) from two separate male/female pairs were genotyped for the inversion. For 47 of 48 individuals, the XY animals were male and the XX animals were female. One male was XX. ( C ) F ST analysis comparing 24 males and 24 females identified chromosome 10 as the primary genetic region that segregated with sex. ( D ) Comparison of heterozygosity leve2ls9o3f 24 male and 24 female animals also identified chromosome 10 as an outlier.

Article Snippet: These differences fall into two primary categories: 1) contigs that were incorrectly ordered or oriented and 2) unplaced contigs that Bionano anchored to specific chromosomes.

Techniques: Comparison