Sensing microbial infections in the Drosophila melanogaster genetic model organism

Immunogenetics, Journal Year: 2022, Volume and Issue: 74(1), P. 35 - 62

Published: Jan. 29, 2022

Language: Английский

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De novosequencing, diploid assembly, and annotation of the black carpenter ant,Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(1), P. 17 - 28

Published: June 21, 2022

The black carpenter ant (Camponotus pennsylvanicus) is a pest species found widely throughout North America. From single individual I used long-read nanopore sequencing to assemble phased diploid genome of 306 Mb and 60X coverage, with quality assessed by 97.0% BUSCO score, improving upon other assemblies. mitochondrial reveals minor rearrangements from ants. reads also allowed assembly parasitic symbiont genomes. include complete Wolbachia bacterial size 1.2 Mb, as well commensal Blochmannia pennsylvanicus, at 791 kb. DNA methylation hydroxymethylation were measured base-pair resolution level the same confirmed extremely low levels seen in Formicidae family. There was moderate heterozygosity, 0.16% bases being biallelic parental haplotypes. Protein prediction yielded 14 415 amino acid sequences 95.8% score 86% matching previously known proteins. All assemblies derived MinION flow cell generating 20 Gb sequence for cost $1047 including consumable reagents. Adding fixed costs equipment brings total an ant-sized less than $5000. analyses performed 1 week on desktop computer.Creating reference animal genomes typically large, expensive process. Here sequenced only $1000 sole researcher just one week. Along nuclear genome, assembled two bacteria living within ant. Nanopore technology enabled epigenetic measurements replicated studies showing very methylation. compared favorably continuity protein accuracy. This method will allow low-resource labs create high cost.

Language: Английский

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Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 2, 2023

Abstract Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed cost-effective hybrid Oxford Nanopore (ONT) long-read Illumina short-read approach used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing number assemblies this taxonomic group. The next challenge address culture bias taxon sampling by that cannot easily be reared lab. Here, we build upon our previous methods perform amplification-free ONT single wild flies obtained either directly field or ethanol-preserved specimens museum collections, improving representation lesser studied taxa whole-genome data. Using Novaseq X Plus P2 sequencers with R10.4.1 chemistry, set new benchmark inexpensive at US $150 per while assembling as little 35 ng genomic DNA fly. present 183 179 resource systematics, phylogenetics, comparative genomics. Of these genomes, 62 are pooled lab strains 121 adult flies. Despite sample limitations working small insects, most single-fly diploid comparable contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), accuracy (>QV40 genome-wide R10.4.1) inbred lines. well-resolved multi-locus phylogeny 360 4 outgroup encompassing publicly available (as August 2023) Finally, Progressive Cactus whole-genome, reference-free alignment built subset 298 suitably high-quality genomes. alignment, along updated protocols computational pipelines, released an open tool studying evolution scale entire insect family.

Language: Английский

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Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA based host defense against invadingP-elements

Genome Research, Journal Year: 2024, Volume and Issue: unknown

Published: March 15, 2024

To prevent the spread of transposable elements (TEs), hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major mechanism operates through PIWI-interacting RNAs (piRNAs). investigate establishment host defense, we introduced P -element, one most widely studied eukaryotic transposons, into naive lines Drosophila erecta . We monitored invasion in three replicates for more than 50 generations by sequencing genomic DNA (using short long reads), small RNAs, transcriptome at regular intervals. A piRNA-based was rapidly established two (R1, R4) but not third (R2), which -element copy numbers kept increasing over generations. found that ping-pong cycle could be activated R2, although is fully functional against other TEs. Furthermore, R2 had both insertions piRNA clusters siRNAs, suggesting neither them sufficient to trigger defense. Our work shows control an invading TE requires activation this stochastic event may fail some populations, leading proliferation TEs ultimately threaten integrity genome.

Language: Английский

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Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 12, 2024

Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved DNA packaging, centromeres that core components chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres ensure integrity, piRNA clusters encoding host defenses against selfish elements, and virtually entire Y chromosome. These formed by similar tandem arrays, pose significant challenges for experimental informatic study, impeding sequence-level descriptions understanding genetic variation. Here, we report assembly variation analysis such regions

Language: Английский

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