Additional file 1: Table S1. of Early evolutionary history and genomic features of gene duplicates in the human genome

Evolutionary and genomic features of 184 gene duplicates with low synonymous divergence in the human genome. (PDF 262 kb

Mutation Accumulation Generation 100 Fitness Data

Productivity and survivorship to adulthood for MA lines following 100 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Mutation Accumulation Generation 409 Fitness Data

Productivity and survivorship to adulthood for MA lines following 409 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Mutation Accumulation Generation 172 Fitness Data

Productivity and survivorship to adulthood for MA lines following 172 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Mutation Accumulation Generation 300 Fitness Data

Productivity and survivorship to adulthood for MA lines following 300 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Phylogeny and domain structure of FReDs in the <i>B</i>. <i>glabrata</i> genome.

Left panel: A ML tree was constructed using full length aa sequences of 80 FReDs. ModelFinder selected WAG+F+R7 as the best-fit model for tree inference (Bayesian Information Criterion). A test of 1,000 bootstrap replicates was performed and nodes with bootstrap support of 60 or higher are marked with different colorss. Right panel: structure of FReD gene products. EGF: epidermal growth factor; IgSF: immunoglobulin superfamily; FBG: fibrinogen domain.</p

Chromosome-level genomic information.

Schistosomiasis is one of the world’s most devastating parasitic diseases, afflicting 251 million people globally. The Neotropical snail Biomphalaria glabrata is an important intermediate host of the human blood fluke Schistosoma mansoni and a predominant model for schistosomiasis research. To fully exploit this model snail for biomedical research, here we report a haplotype-like, chromosome-level assembled and annotated genome of the homozygous iM line of B. glabrata that we developed at the University of New Mexico. Using multiple sequencing platforms, including Illumina, PacBio, and Omni-C sequencing, 18 sequence contact matrices representing 18 haploid chromosomes (2n = 36) were generated (337x genome coverage), and 96.5% of the scaffold sequences were anchored to the 18 chromosomes. Protein-coding genes (n = 34,559), non-coding RNAs (n = 2,406), and repetitive elements (42.52% of the genome) were predicted for the whole genome, and detailed annotations for individual chromosomes were also provided. Using this genomic resource, we have investigated the genomic structure and organization of the Toll-like receptor (TLR) and fibrinogen-domain containing protein (FReD) genes, the two important immune-related gene families. Notably, TLR-like genes are scattered on 13 chromosomes. In contrast, almost all (39 of 40) fibrinogen-related genes (FREPs) (immunoglobulin superfamily (IgSF) + fibrinogen (FBG)) are clustered within a 5-million nucleotide region on chromosome 13, yielding insight into mechanisms involved in the diversification of FREPs. This is the first genome of schistosomiasis vector snails that has been assembled at the chromosome level, annotated, and analyzed. It serves as a valuable resource for a deeper understanding of the biology of vector snails, especially Biomphalaria snails.</div

Distribution of <i>TLR</i> genes on <i>B</i>. <i>glabrata</i> chromosomes.

The number in parenthesis is the number of TLR genes identified on the chromosome. Only chromosomes possessing TLR are shown.</p

Fig 2 -

Synteny plot analyses show the comparison among the 18 chromosomes (A) and between the 18 chromosome-level assemblies and the 18 LGs (B). Blue and pink rectangles show matches in the same and reverse directions, respectively. The chromosome- and scaffold-level assemblies for the iM line of B. glabrata were compared at the nucleotide level using Minimap2.</p

Phylogenetic relationship of 39 <i>FREPs</i> and their locations on chromosome 13.

The ML tree was constructed with 1,000 bootstrap replicates. ModelFinder selected JTT+F+R4 as the best-fit model for tree inference (Bayesian Information Criterion). A test of 1,000 bootstrap replicates was performed and nodes with bootstrap support of 60 or higher are indicated by different colors FREP genes are grouped into 3 large clusters, in which their sequences are indicated by purple, green, and orange lines, respectively.</p