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Towards the investigation of the adaptive divergence in a species of exceptional ecological plasticity [Elektronski vir] : chromosome-scale genome assembly of Chouardia litardierei (Hyacinthaceae)Radosavljević, Ivan, 1981- ...One of the central goals of evolutionary biology is to understand the genomic basis of adaptive divergence. Different aspects of evolutionary processes should be studied through genome-wide ... approaches, therefore maximizing the investigated genomic space. However, in-depth genome-scale analyses often are restricted to a model or economically important species and their closely related wild congeners with available reference genomes. Here, we present the high-quality chromosome-level genome assembly of Chouardia litardierei, a plant species with exceptional ecological plasticity. By combining PacBio and Hi-C sequencing technologies, we generated a 3.7 Gbp genome with a scaffold N50 size of 210 Mbp. Over 80% of the genome comprised repetitive elements, among which the LTR retrotransposons prevailed. Approximately 86% of the 27,257 predicted genes were functionally annotated using public databases. For the comparative analysis of different ecotypes’ genomes, the whole-genome sequencing of two individuals, each from a distinct ecotype, was performed. The detected above-average SNP density within coding regions suggests increased adaptive divergence-related mutation rates, therefore confirming the assumed divergence processes within the group. The constructed genome presents an invaluable resource for future research activities oriented toward the investigation of the genetics underlying the adaptive divergence that is likely unfolding among the studied species’ ecotypes.Source: International journal of molecular sciences [Elektronski vir]. - ISSN 1422-0067 (Vol. 24, no. 13, art. 10755, 2023, 16 str.)Type of material - e-article ; adult, seriousPublish date - 2023Language - englishCOBISS.SI-ID - 160619011
Author
Radosavljević, Ivan, 1981- |
Križanović, Krešimir |
Šarančić, Sara Laura |
Jakše, Jernej
Topics
Chouardia litardierei |
PacBio |
Hi-C |
chromosome-level genome |
draft genome |
local adaptation |
adaptivna divergenca |
Chouardia litardierei |
bioinformatika |
sekvenciranje genoma |
molekularne tehnike
Author | Radosavljević, Ivan, 1981- ... |
Title | Towards the investigation of the adaptive divergence in a species of exceptional ecological plasticity [Elektronski vir] : chromosome-scale genome assembly of Chouardia litardierei (Hyacinthaceae) |
Publication date | 2023-06-28 |
COBISS.SI-ID | 160619011 |
Publication version in repository | Publisher's version |
Publication licence | Creative Commons Attribution 4.0 International |
Embargo | Immediate publication for public |
Project(s) from which the publication was funded
Title | Acronym | Project ID | Funder |
---|---|---|---|
Amethyst Meadow Squill (Chouardia litardierei, Hyacinthaceae): a study system for ecological divergence” | HRZZ-IP-2020-02-8099 |
Croatian Science Foundation (CSF) |
|
Single-genome and metagenome de novo assembly | HRZZ-IP-2018-01-5886 |
Croatian Science Foundation (CSF) |
Files that belong to the publication
Link |
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https://www.mdpi.com/1422-0067/24/13/10755 |
https://repozitorij.uni-lj.si/IzpisGradiva.php?id=148238 |
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Database name | Field | Year |
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Links to authors' personal bibliographies | Links to information on researchers in the SICRIS system |
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Radosavljević, Ivan, 1981- | |
Križanović, Krešimir | |
Šarančić, Sara Laura | |
Jakše, Jernej | 16379 |
Source: Personal bibliographies
and: SICRIS
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