Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome DOI Creative Commons

Harsh Shukla,

Mahul Chakraborty, J. J. Emerson

et al.

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

Towards population-scale long-read sequencing DOI Open Access
Wouter De Coster, Matthias H. Weissensteiner, Fritz J. Sedlazeck

et al.

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 22(9), P. 572 - 587

Published: May 28, 2021

Language: Английский

Citations

256
Widespread introgression across a phylogeny of 155 Drosophila genomes DOI Creative Commons
Anton Suvorov, Bernard Kim, Jeremy Wang

et al.

Current Biology, Journal Year: 2021, Volume and Issue: 32(1), P. 111 - 123.e5

Published: Nov. 16, 2021

Language: Английский

Citations

228
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation DOI Creative Commons
Xiaoling Tong, Min-Jin Han, Kunpeng Lu

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Sept. 24, 2022

Abstract The silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. currently available genomes limit understanding its genetic diversity and discovery valuable alleles breeding. Here, we deeply re-sequence 1,078 silkworms assemble long-read 545 representatives. We construct a high-resolution pan-genome dataset representing almost entire genomic content in silkworm. find that population harbors high density variants identify 7308 new genes, 4260 (22%) core 3,432,266 non-redundant structure variations (SVs). reveal hundreds genes SVs may contribute to artificial selection (domestication breeding) Further, focus on four responsible, respectively, two (silk yield silk fineness) ecologically adaptive traits (egg diapause aposematic coloration). Taken together, our population-scale resources will promote functional genomics studies breeding improvement

Language: Английский

Citations

87
Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae DOI Creative Commons
Samuel O’Donnell, Jia‐Xing Yue, Omar Abou Saada

et al.

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(8), P. 1390 - 1399

Published: July 31, 2023

Pangenomes provide access to an accurate representation of the genetic diversity species, both in terms sequence polymorphisms and structural variants (SVs). Here we generated Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing species' phylogenetic ecological diversity. The ScRAP includes phased haplotype assemblies several heterozygous diploid polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that a broad view genomic diversity, including dynamics telomere length transposable elements. uncovered frequent cases complex aneuploidies where large chromosomes underwent deletions translocations. found can impact gene expression near breakpoints substantially contribute repertoire evolution. also discovered horizontally acquired regions insert at chromosome ends generate new telomeres. Overall, demonstrates benefit pangenome understanding genome evolution population scale.

Language: Английский

Citations

67
Ecology-relevant bacteria drive the evolution of host antimicrobial peptides in Drosophila DOI
Mark A. Hanson, L. Grollmus, Bruno Lemaître

et al.

Science, Journal Year: 2023, Volume and Issue: 381(6655)

Published: July 20, 2023

Antimicrobial peptides are host-encoded immune effectors that combat pathogens and shape the microbiome in plants animals. However, little is known about how host antimicrobial peptide repertoire adapted to its microbiome. Here, we characterized function evolution of Diptericin family Diptera. Using mutations affecting two Diptericins ( Dpt ) Drosophila melanogaster , reveal specific role DptA for pathogen Providencia rettgeri DptB gut mutualist Acetobacter . The presence DptA- or DptB- like genes across Diptera correlates with their environment. Moreover, sequences predict resistance against infection by these bacteria genus Our study explains evolutionary logic behind bursts rapid an reveals adapts changing microbial environments.

Language: Английский

Citations

57
DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics DOI Creative Commons

Cédric Finet,

Victoria A. Kassner,

Antonio Bernardo Carvalho

et al.

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 13(8)

Published: Aug. 1, 2021

Abstract The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. whole family Drosophilidae, which contains over 4,400 species, offers plethora of cases comparative evolutionary studies. Despite long history phylogenetic inference, many relationships remain unresolved among the genera, subgenera, species groups in Drosophilidae. To clarify these relationships, we first developed set new genomic markers assembled multilocus data 17 genes from 704 We then inferred tree with highly supported this family. Additionally, were able to determine position some previously unplaced species. These results establish framework investigating evolution traits fruit flies, as well valuable resources systematics.

Language: Английский

Citations

63
Hematopoietic plasticity mapped in Drosophila and other insects DOI Creative Commons
Dan Hultmark, István Andó

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Aug. 3, 2022

Hemocytes, similar to vertebrate blood cells, play important roles in insect development and immunity, but it is not well understood how they perform their tasks. New technology, particular single-cell transcriptomic analysis combination with

Language: Английский

Citations

43
Expansion and loss of sperm nuclear basic protein genes in Drosophila correspond with genetic conflicts between sex chromosomes DOI Creative Commons
Ching-Ho Chang,

Isabel Mejia Natividad,

Harmit S. Malik

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Feb. 10, 2023

Many animal species employ sperm nuclear basic proteins (SNBPs) or protamines to package genomes tightly. SNBPs vary across lineages and evolve rapidly in mammals. We used a phylogenomic approach investigate SNBP diversification Drosophila species. found that most genes melanogaster under positive selection except for essential male fertility. Unexpectedly, evolutionarily young are more likely be critical fertility than ancient, conserved genes. For example, CG30056 is dispensable despite being one of three universally retained 19 independent gene amplification events occurred preferentially on sex chromosomes. Conversely, the montium group lost otherwise-conserved genes, coincident with an X-Y chromosomal fusion. Furthermore, became linked chromosomes via fusions were degenerate relocate back autosomes. hypothesize autosomal suppress meiotic drive, whereas sex-chromosomal expansions lead drive. render by making X-versus-Y drive obsolete costly. Thus, genetic conflicts between may rapid evolution during spermatogenesis

Language: Английский

Citations

29
Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2 DOI Creative Commons

Q X Charles Mak,

Ryan R. Wick, James Holt

et al.

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(3)

Published: March 1, 2023

Abstract As the accuracy and throughput of nanopore sequencing improve, it is increasingly common to perform long-read first de novo genome assemblies followed by polishing with accurate short reads. We briefly introduce FMLRC2, successor original FM-index Long Read Corrector (FMLRC), illustrate its performance as a fast assembly polisher for both bacterial eukaryotic genomes.

Language: Английский

Citations

23
Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life DOI Creative Commons
Bernard Kim, Hannah R. Gellert, Samuel H. Church

et al.

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(7), P. e3002697 - e3002697

Published: July 18, 2024

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 (>1 Mb 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

Citations

16