Towards the investigation of the adaptive divergence in a species of exceptional ecological plasticity : chromosome-scale genome assembly of Chouardia litardierei (Hyacinthaceae)

Radosavljević, Ivan (author), Križanović, Krešimir (author), Šarančić, Sara Laura (author), Jakše, Jernej (author)

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.

• Language: English
• Keywords: Chouardia litardierei, PacBio, Hi-C, chromosome-level genome, draft genome, local adaptation
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2023
• Number of pages: 16 str.
• Numbering: Vol. 24, no. 13, art. 10755
• PID: 20.500.12556/RUL-148238
• UDC: 577.2
• ISSN on article: 1422-0067
• COBISS.SI-ID: 160619011
• Publication date in RUL: 04.08.2023

Record is a part of a journal

• Title: International journal of molecular sciences
• Shortened title: Int. j. mol. sci.
• Publisher: MDPI
• ISSN: 1422-0067
• COBISS.SI-ID: 2779162

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: adaptivna divergenca, Chouardia litardierei, bioinformatika, sekvenciranje genoma, molekularne tehnike

Projects

• Funder: HRZZ - Croatian Science Foundation
• Funding programme: Croatian Science Foundation (CSF)
• Project number: HRZZ-IP-2020-02-8099
• Name: Amethyst Meadow Squill (Chouardia litardierei, Hyacinthaceae): a study system for ecological divergence”

• Funder: HRZZ - Croatian Science Foundation
• Funding programme: Croatian Science Foundation (CSF)
• Project number: HRZZ-IP-2018-01-5886
• Name: Single-genome and metagenome de novo assembly