The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes.

"plos publication stage vor-update-to-uncorrected-proof publication update 2024-01-26 data availability the l sigmodontis pacbio hifi data are available at ena under the accession err11560319.; the nxlitsigm11 1 reference genome is available under the bioproject prjeb64423.; the alternate haplotype assembly is available under the bioproject prjeb64424.; data availability the l sigmodontis pacbio hifi data are available at ena under the accession err11560319.; the nxlitsigm11 1 reference genome is available under the bioproject prjeb64423.; the alternate haplotype assembly is available under the bioproject prjeb64424.; normalised coverage ( n ) was calculated by dividing the coverage in each 100 kb window by the median autosomal coverage (c) distribution of counts of busco genes in 500 kb windows in the six l sigmodontis chromosomes coloured by their allocation to the seven nigon elements (a-e n x) 10 1371/journal pgen 1011116 t001 table 1 accession information species litomosoides sigmodontis dirofilaria immitis onchocerca volvulus brugia malayi bioproject prjeb64423 - prjeb513 prjna10729 reference this work [ ] [ ] [ ] reference genome metrics span (mb) 65 9 89 4 96 4 88 2 scaffolds (n) 6 (+mt) 27 708 197 scaffold n50 (mb) 10 9 15 2 25 5 14 2 span in chromosome-sized scaffolds (%) 100 0 98 6 3 94 3 92 1 contigs (n) 1 28 167 1006 205 contig n50 (mb) 1 5 0 4 2 1 0 10 3 busco completeness (%) 2 96 0 90 1 97 7 98 2 busco duplication (%) 2 0 4 0 5 0 9 0 6 qv 52 9 - - - gene set metrics number of protein-coding genes9686 no gene set available 12109 10878 number of transcripts11646 no gene set available 13436 15985 busco completeness (%) 2 95 7 no gene set available 98 2 98 9 1. file s1 table (xlsx"

"code and intermediate files associated with the analyses and figures are available at https://github com/lstevens17/litomosoides_ms .; code and intermediate files associated with the analyses and figures are available at https://github com/lstevens17/litomosoides_ms .; we randomly subsampled 10% of the male hi-c reads using samtools1 14 [ ] and aligned them to the hifiasm primary assembly using bwa mem 0 7 17-r1188 [ ] filtered out pcr duplicates using picard 2 27 1-0 (available at http://broadinstitute github io/picard/ ) and scaffolded the assembly using yahs [ ].; we manually curated the scaffolded assembly as in [ ] and used pretextview 0 2 5 (available at https://github com/wtsi-hpag/pretextview ) to manually inspect the hi-c signal.; a final hi-c contact map was generated using juicer 2 0 [ ] and juicebox 1 11 08 (available at https://github com/aidenlab/juicebox ) and is shown in fig 1a .; we used buscopainter (available at https://github com/lstevens17/buscopainter ) to assign each busco gene to a nigon element as defined by [ ].; to infer a filarial phylogeny we used busco2fasta (available at https://github com/lstevens17/busco2fasta ) to identify and extract the protein sequences of 1757 busco genes that were single-copy in the nxlitsigm11 1 reference genomes and genomes of ten other filarial species ( s2 table ).; we aligned the protein sequences using fsa 1 15 9 [ ] and concatenated the alignments of each single-copy orthogroup into a supermatrix using catfasta2phyml v1 1 0 (available at https://github com/nylander/catfasta2phyml )."

"The authors have declared that no competing interests exist."

"This work was supported by Wellcome Trust (https://wellcome.org/) Grants 206194 and 218328 awarded to the Wellcome Sanger Institute. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. L. sigmodontis maintenance at the University of Manchester was funded by the Medical Research Council UK (MR/K01207X/1) (https://www.ukri.org/councils/mrc/) and Wellcome Trust (106898/A/15/Z) (https://wellcome.org/) awarded to JA. The funders played no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript."