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opencc-zeroAug 2023View details →

Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata

Wild wheat relatives have been explored in plant breeding to increase the genetic diversity of bread wheat, one of the most important food crops. Aegilops umbellulata is a diploid U genome-containing grass species that serves as a genetic reservoir for wheat improvement. In this study, we report the construction of a chromosome-scale reference assembly of Ae. umbellulata accession TA1851 based on corrected PacBio HiFi reads and chromosome conformation capture. The total assembly size was 4.25 Gb with a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We benchmarked the performance of hifiasm and LJA, two of the most widely used assemblers using standard and corrected HiFi reads, revealing a positive effect of corrected input reads. Comparative genome analysis confirmed substantial chromosome rearrangements in Ae. umbellulata compared to bread wheat. In summary, the Ae. umbellulata assembly provides a resource for comparative genomics in Triticeae and for the discovery of agriculturally important genes.

zenodo36/100

Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation : simulated data

Data simulated with Aevol (<a href="http://www.aevol.fr">www.aevol.fr</a>), a software available on gitlab ( <a href="https://gitlab.inria.fr/aevol/aevol">https://gitlab.inria.fr/aevol/aevol</a> ), for our paper submitted to Molecular Ecology entitled "Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation".

opencc-by-4.0Aug 2023View details →

opencc-zeroSep 2023View details →

The X chromosome of insects likely predates the origin of Class Insecta

Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.

opencc-zeroOct 2023View details →

Data from: Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies

Large-scale chromosome rearrangements, such as fissions and fusions, are a common feature of eukaryote evolution. They can have considerable influence on the evolution of populations, yet it remains unclear exactly how rearrangements become established and eventually fix. Rearrangements could fix by genetic drift if they are weakly deleterious or neutral, or they may instead be favoured by positive natural selection. Here we compare genome assemblies of three closely related Brenthis butterfly species and characterise a complex history of fission and fusion rearrangements. An inferred demographic history of these species suggests that rearrangements became fixed in populations with large long-term effective size (Ne). However, we also find large runs of homozygosity within individual genomes and show that a model of population structure with smaller local Ne can reconcile these observations. Using a recently developed analytic framework for characterising hard selective sweeps, we find that chromosome fusions are not enriched for evidence of past sweeps compared to other regions of the genome. Nonetheless, one chromosome fusion in the B. daphne genome is associated with a valley of diversity where genealogical branch lengths are distorted, consistent with a selective sweep. Our results suggest that drift is a stronger force in these populations than suggested by overall genetic diversity, but that the fixation of strongly underdominant rearrangements remains unlikely. Additionally, although chromosome fusions do not typically exhibit signatures of selective sweeps, a single example raises the possibility that natural selection may sometimes play a role in their fixation.

Nilotinib in Newly Diagnosed Adult Philadelphia Chromosome & /or BCR-ABL Positive Chronic Myeloid Leukaemia in Chronic Phase

ClinicalTrials.gov study NCT01061177. IPD Sharing: Not stated. Countries: 26. Publications: 2.

controlledIPD-YESFeb 2026View details →

Safety And Efficacy Study Of Bosutinib In Patients With Philadelphia Chromosome Positive Chronic Myeloid Leukemia Previously Treated With One Or More Tyrosine Kinase Inhibitors

ClinicalTrials.gov study NCT02228382. IPD Sharing: YES. Countries: 8. Publications: 5.

Lenalidomide in Older Patients With Acute Myeloid Leukemia Without Chromosome 5q Abnormalities

ClinicalTrials.gov study NCT00546897. IPD Sharing: Not stated. Countries: 1. Publications: 4.

Study of Molecular Response in Adult Patients on Nilotinib With Philadelphia Chromosome Positive Chronic Myelogenous Leukemia (Ph+ CML) in Chronic Phase and a Suboptimal Molecular Response to Imatinib

ClinicalTrials.gov study NCT00644878. IPD Sharing: Not stated. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

Compare Bosutinib To Imatinib In Subjects With Newly Diagnosed Chronic Phase Philadelphia Chromosome Positive CML

ClinicalTrials.gov study NCT00574873. IPD Sharing: YES. Countries: 29. Publications: 7.

Vaccine Therapy in Treating Patients With Philadelphia Chromosome-Positive Chronic Myelogenous Leukemia

ClinicalTrials.gov study NCT00466726. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Safety and Efficacy of Imatinib Versus Interferon-α Plus Cytarabine in Patients With Newly Diagnosed Philadelphia Chromosome Positive Chronic Myelogenous Leukemia

ClinicalTrials.gov study NCT00333840. IPD Sharing: Not stated. Countries: 16. Publications: 3.

Study Evaluating SKI-606 (Bosutinib) In Philadelphia Chromosome Positive Leukemias

ClinicalTrials.gov study NCT00261846. IPD Sharing: Not stated. Countries: 27. Publications: 13.

Study Evaluating SKI-606 (Bosutinib) In Japanese Subjects With Philadelphia Chromosome Positive Leukemias

ClinicalTrials.gov study NCT00811070. IPD Sharing: Not stated. Countries: 1. Publications: 3.