SAMN35107261
External Id
Carnegie Institution for Science
INSDC center name
2023-05-16T00:00:00Z
INSDC first public
2023-05-23T12:54:59.024Z
INSDC last update
live
INSDC status
Invertebrate
NCBI submission model
Invertebrate.1.0
NCBI submission package
mixed adult
age
Laboratories of Laura Ross and Allan Spradling
biomaterial_provider
Holo2
breed
Robert B. Baird and John M. Urban
collected_by
2019/2021
collection_date
This sample group is the combination of the following individual BioSamples: SAMN34115883, SAMN35060802, SAMN35060803.
derived from
The inverted region of the X' (X-prime) was assembled using X'X DNA samples from Bradysia coprophila (fungus gnats) cultured in two separate laboratories. John Urban in the Spradling Laboratory (Baltimore, MD) provided Illumina data from whole adult X'X females (BioSample SAMN34115883). Robert Baird in the Ross Laboratory (Edinburgh, United Kingdom) provided Illumina and PacBio data from adult X'X female heads (BioSamples SAMN35060802, SAMN35060803). Overall, this sample group is the combination of the following individual BioSamples: SAMN34115883, SAMN35060802, SAMN35060803. However, the pre-assembly methods for fishing out X'-specific reads also included a comparison to fungus gnats negative for the X' chromosome, namely XO males (BioSamples SAMN34115808). Briefly, the assembly pipeline was as follows: (1) 27-mers in XO male and X'X Illumina datasets were counted with KMC3, (2) 27-mers that are putatively specific to the X' inversion region (X'-inversion-specific 27-mers) were identified using KAT (e.g. frequency of 0 in XO male reads and >5 in X'X female reads to exclude error 27-mers ). (3) Cookiecutter was used to to extract X'-inversion-specific reads given X'-specific 27-mers. (4) The X'-inversion-specific reads were assembled into X'-inversion-specific contigs using SPAdes (v3.14.1). (5) The X'-inversion-specific contigs were scaffolded using RagTag (v2.1.0) and the available X-chromosome scaffold as a reference (CM025456.2 from GCA_014529535.2 / VSDI00000000.2 ; Urban et al, 2021 and 2022) ; contigs that failed to scaffold were discarded. (6) The X'-inversion-scaffold was gap-filled and polished with X'-attracted reads in the presence of the entire genome as a competitor for alignments. In other words, only reads that had best-alignments to the X' inversion region in the presence of the X chromosome and the entire genome were used for gap-filling and polishing. This was done specifically the following way. The inversion scaffold was combined with the currently-available chromosome-scale assembly that contains single scaffolds for chromosomes X, II, III, and IV as well as unplaced associated contigs (GCA_014529535.2 ; VSDI00000000.2 ; Urban et al, 2021 and 2022) to produce an X'X genome. PacBio long reads from X'X females were mapped to this X'X genome with Minimap2 (v2.17-r941) and gaps were filled using RaCon (v1.4.20). Illumina reads from X'X females were subsequently mapped to the X'X genome with Minimap2 and RaCon was used to polish the assembly.
description
mixed adult
dev_stage
X'X
genotype
USA: Baltimore, MD; United Kingdom, Edinburgh
geo_loc_name
Bradysia coprophila stocks were originally obtained from Susan Gerbi and subsequently cultured independently in the Ross and Spradling Laboratories; These Holo2 stocks descend from Sciara coprophila cultures started by Charles Metz and colleagues in the 1920s.
history of lab stock
whole adults and adult heads
host_tissue_sampled
Robert B. Baird and John M. Urban
identified_by
Lab stocks, Carnegie Institution for Science, Department of Embryology, Spradling Laboratory, Baltimore, MD ; and Edinburgh University, Ross Laboratory, Edinburgh, UK
isolation_source
Bradysia coprophila
http://purl.obolibrary.org/obo/NCBITaxon_38358
organism
female
sex
female
sex of offspring
18-21*C
temp
whole adults and adult heads
tissue
Samples used for assembling the first model sequence for the ~55 Mb X' long paracentric inversion region
title