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Towards the investigation of the adaptive divergence in a species of exceptional ecological plasticity : chromosome-scale genome assembly of Chouardia litardierei (Hyacinthaceae)
ID
Radosavljević, Ivan
(
Avtor
),
ID
Križanović, Krešimir
(
Avtor
),
ID
Šarančić, Sara Laura
(
Avtor
),
ID
Jakše, Jernej
(
Avtor
)
PDF - Predstavitvena datoteka,
prenos
(6,35 MB)
MD5: C6AC140248A4A6C34B5ED659DC13B258
URL - Izvorni URL, za dostop obiščite
https://www.mdpi.com/1422-0067/24/13/10755
Galerija slik
Izvleček
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.
Jezik:
Angleški jezik
Ključne besede:
Chouardia litardierei
,
PacBio
,
Hi-C
,
chromosome-level genome
,
draft genome
,
local adaptation
Vrsta gradiva:
Članek v reviji
Tipologija:
1.01 - Izvirni znanstveni članek
Organizacija:
BF - Biotehniška fakulteta
Status publikacije:
Objavljeno
Različica publikacije:
Objavljena publikacija
Leto izida:
2023
Št. strani:
16 str.
Številčenje:
Vol. 24, no. 13, art. 10755
PID:
20.500.12556/RUL-148238
UDK:
577.2
ISSN pri članku:
1422-0067
COBISS.SI-ID:
160619011
Datum objave v RUL:
04.08.2023
Število ogledov:
756
Število prenosov:
26
Metapodatki:
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Objavi na:
Gradivo je del revije
Naslov:
International journal of molecular sciences
Skrajšan naslov:
Int. j. mol. sci.
Založnik:
MDPI
ISSN:
1422-0067
COBISS.SI-ID:
2779162
Licence
Licenca:
CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
Povezava:
http://creativecommons.org/licenses/by/4.0/deed.sl
Opis:
To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.
Sekundarni jezik
Jezik:
Slovenski jezik
Ključne besede:
adaptivna divergenca
,
Chouardia litardierei
,
bioinformatika
,
sekvenciranje genoma
,
molekularne tehnike
Projekti
Financer:
HRZZ - Croatian Science Foundation
Program financ.:
Croatian Science Foundation (CSF)
Številka projekta:
HRZZ-IP-2020-02-8099
Naslov:
Amethyst Meadow Squill (Chouardia litardierei, Hyacinthaceae): a study system for ecological divergence”
Financer:
HRZZ - Croatian Science Foundation
Program financ.:
Croatian Science Foundation (CSF)
Številka projekta:
HRZZ-IP-2018-01-5886
Naslov:
Single-genome and metagenome de novo assembly
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