Sciara Genome
The Sciara genome contains 3 pairs of autosomes (chromosomes II, III and IV), two sex chromosomes (X and X’), and 2 germ line limited L chromosomes. The older estimate of 211 Mb for the size of the Sciara haploid somatic genome containing the X and three autosomes but no L chromosomes has been increased somewhat to 274 Mb (Rasch 2006).
John Urban, a former graduate student in the Gerbi lab at Brown, has completed the sequence of the Sciara (Bradysia coprophila) genome and transcriptome using Illumina, PacBio, the Oxford Nanopore Technologies MinION, and BioNano Genomics Irys scaffolding (Urban et al. 2021). We have used fluorescence in situ hybridization (FISH) to map sequences to Sciara polytene chromosomes, thus anchoring the sequence map on the chromosome map as well as validating the genome assembly. Sequences are also available for the Sciara germline restricted L chromosomes (Hodson et al. 2022). Useful links for the Sciara genome sequence are listed below:
i5k Workspace:
(1) Organism page: https://i5k.nal.usda.gov/bradysia-coprophila
(2) Blast: https://i5k.nal.usda.gov/webapp/blast
(3) Apollo/Jbrowse: https://apollo.nal.usda.gov/apollo/Bradysia_coprophila/jbrowse/
(4) Apollo registration: https://i5k.nal.usda.gov/web-apollo-registration
(5) Gene pages: https://i5k.nal.usda.gov/search/site/Bradysia%20coprophila%20AND%20gene
Genome links for NCBI:
(1) BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA291918/
(2) BioSample: https://www.ncbi.nlm.nih.gov/bioproject?LinkName=biosample_bioproject&from_uid=12529675
(3) Genbank: https://www.ncbi.nlm.nih.gov/assembly/GCA_014529535.1
(4) RefSeq: https://www.ncbi.nlm.nih.gov/assembly/GCF_014529535.1
(5) Project version; https://www.ncbi.nlm.nih.gov/nuccore/VSDI00000000.1/
(6) De novo transcriptome: https://www.ncbi.nlm.nih.gov/nuccore/2076772316
(7) Associated bacterial sequences: https://www.ncbi.nlm.nih.gov/nuccore/JAHXDM000000000.1
(8) Submissions from Christina Hodson and Laura Ross: https://www.ncbi.nlm.nih.gov/bioproject/733987
The NCBI annotation is described here:
(1) https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Bradysia_coprophila/100/
(2) https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/38358/100/
NCBI Genome Browser for the genome:
https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_014529535.1
NCBI BLAST the genome:
Datasets on SRA:
https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP218121
On the Taxonomy Browser:
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=38358
Maker2 annotation dataset from Ag Data Commons:
(1) https://data.nal.usda.gov/dataset/bradysia-coprophila-genome-annotations-bcopv10
Links for the Sciara L chromosome sequence data:
Sequence read data has been submitted to ENA under accession number PRJEB44837. The repository https://github.com/RossLab/Bradysia-GRCs and zenodo archive https://doi.org/10.5281/zenodo.5884857 contain scripts associated with this project. Data tables to generate figures and supplementary figures are available at https://github.com/RossLab/Bradysia-GRCs/tables/figure_data.tar.gz and https://doi.org/10.5281/zenodo.5884857.