ORCID Profile
0000-0001-5119-1837
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Publisher: Springer Science and Business Media LLC
Date: 04-2019
DOI: 10.1038/S41559-019-0850-1
Abstract: Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence ergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting ersified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.
Publisher: Springer Science and Business Media LLC
Date: 27-11-2019
DOI: 10.1038/S42003-019-0634-9
Abstract: A new avenue of mining published genome-wide association studies includes the joint analysis of related traits. The power of this approach depends on the genetic correlation of traits, which reflects the number of pleiotropic loci, i.e. genetic loci influencing multiple traits. Here, we applied new meta-analyses of optic nerve head (ONH) related traits implicated in primary open-angle glaucoma (POAG) intraocular pressure and central corneal thickness using Haplotype reference consortium imputations. We performed a multi-trait analysis of ONH parameters cup area, disc area and vertical cup-disc ratio. We uncover new variants rs11158547 in PPP1R36-PLEKHG3 and rs1028727 near SERPINE3 at genome-wide significance that replicate in independent Asian cohorts imputed to 1000 Genomes. At this point, validation of these variants in POAG cohorts is h ered by the high degree of heterogeneity. Our results show that multi-trait analysis is a valid approach to identify novel pleiotropic variants for ONH.
Publisher: Cold Spring Harbor Laboratory
Date: 08-12-2019
DOI: 10.1101/867069
Abstract: The tuatara ( Sphenodon punctatus ), the only living member of the archaic reptilian order Rhynchocephalia (Sphenodontia) once widespread across Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New Zealand. A key link to the now extinct stem reptiles from which dinosaurs, modern reptiles, birds and mammals evolved, the tuatara provides exclusive insights into the ancestral amniotes. The tuatara genome, at ∼5 Gbp, is among the largest vertebrate genomes assembled. Analysis of this genome and comparisons to other vertebrates reinforces the uniqueness of the tuatara. Phylogenetic analyses indicate tuatara erged from the snakes and lizards ∼250 MYA. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Genome sequence analysis identifies expansions of protein, non-protein-coding RNA families, and repeat elements, the latter of which show an extraordinary amalgam of reptilian and mammalian features. Sequencing of this genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. It also provides important insights into both the technical challenges and the cultural obligations associated with genome sequencing.
Publisher: Springer Science and Business Media LLC
Date: 18-08-2020
DOI: 10.1038/S41586-020-2661-6
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher: Springer Science and Business Media LLC
Date: 05-08-2020
DOI: 10.1038/S41586-020-2561-9
Abstract: The tuatara ( Sphenodon punctatus )—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana 1,2 —is an iconic species that is endemic to New Zealand 2,3 . A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes 2,4 . Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage erged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
Publisher: Springer Science and Business Media LLC
Date: 04-04-2016
DOI: 10.1038/NG.3540
Abstract: Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study (GWAS) followed by replication in a combined total of 10,503 PACG cases and 29,567 controls drawn from 24 countries across Asia, Australia, Europe, North America, and South America. We observed significant evidence of disease association at five new genetic loci upon meta-analysis of all patient collections. These loci are at EPDR1 rs3816415 (odds ratio (OR) = 1.24, P = 5.94 × 10(-15)), CHAT rs1258267 (OR = 1.22, P = 2.85 × 10(-16)), GLIS3 rs736893 (OR = 1.18, P = 1.43 × 10(-14)), FERMT2 rs7494379 (OR = 1.14, P = 3.43 × 10(-11)), and DPM2-FAM102A rs3739821 (OR = 1.15, P = 8.32 × 10(-12)). We also confirmed significant association at three previously described loci (P < 5 × 10(-8) for each sentinel SNP at PLEKHA7, COL11A1, and PCMTD1-ST18), providing new insights into the biology of PACG.
Publisher: Wiley
Date: 10-10-2020
Publisher: Cold Spring Harbor Laboratory
Date: 02-01-2022
DOI: 10.1101/2021.12.31.473444
Abstract: Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study, we used a combination of long-read and linked-read genome assemblies to investigate the occurrence of insertions and deletions across the chromosomes of 14 species of birds-of-paradise and two species of estrildid finches including highly repetitive W chromosomes. The species s ling encompasses most genera and representatives from all major clades of birds-of-paradise, allowing comparisons between in iduals of the same species, genus, and family. We found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple in iduals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.
Publisher: Springer Science and Business Media LLC
Date: 19-03-2020
DOI: 10.1038/S42003-020-0802-Y
Abstract: Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 in iduals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11 / FBLN2 rs2630445, RBP3 rs11204213) others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.
Publisher: Wiley
Date: 14-05-2022
DOI: 10.1111/MEC.16484
Abstract: Satellite DNA (satDNA) is a fast‐evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short‐ and long‐read data to explore the ersity and evolution of satDNA between in iduals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds‐of‐paradise (Paradisaeidae) and crow ( Corvus ) species. These avian species highlighted the presence of a GC‐rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly erged between closely related species while the satDNA appeared more similar between birds‐of‐paradise species belonging to different genera.
No related grants have been discovered for Valentina Peona.