Naslov
Chouardia litardierei (Hyacinthaceae) genome sequence

Autori
Šarančić, Sara Laura ; Križanović, Krešimir ; Jakše, Jernej ; Radosavljević, Ivan

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
Book of Abstracts / Vuković, Nina ; Šegota, Vedran - Zagreb, 2022, 56-56

ISBN
978-953-8097-03-4

Skup
7. hrvatski botanički simpozij

Mjesto i datum
Zagreb, Hrvatska, 12.09.2022. - 14.09.2022

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
draft genome assembly, Chouardia litardierei

Sažetak
Valuable knowledge of the mechanisms of the speciation, one of the evolution's fundamental processes, could be gained by exploring complex interactions among environment, phenotype, epigenotype, and genotype in a species characterized by exceptional ecological plasticity. For gathering as much information as possible on this subject, amethyst meadow squill (Chouardia litardierei, Hyacinthaceae), a species characterized by extreme ecological plasticity, was chosen as a study system. In-depth analysis of various aspects of local adaptation and divergence processes requires the availability of a studied species' draft genome assembly, so that (epi)genome annotations essential for interpretations of ecotypes characteristics can be performed. Here we report a high-quality genome sequence of Chouardia litardierei. The species has n=13 chromosomes and is characterized by a large genome with an estimated size of 4.1 Gb. Genome sequences were generated using Pacific Bioscience HiFi technology. 6, 526, 182 Hi-Fi reads with a total size of 94.54 Gb and an average read length of 14.5 Kb were obtained. Sequences were assembled into contigs using the hifiasm software (v. 0.16.1-r375). Chromosomal assemblies were generated with Illumina Hi-C reads (1.72 billion reads, 432.3 Gb) using the Juicer, 3d-dna, and Juicebox scaffolding tools. The final assembly comprised 13 main scaffolds, thus being in agreement with the expected chromosome number. The average GC content is 42.9%. BUSCO analysis confirmed the high completeness of the assembly, as only 2.6% of the liliopsida_odb10 dataset was missing. The high proportion of genome repeats was confirmed. RepeatMasker screening against the curated libraries for Viridiplantae repeats (Dfam and Repbase) revealed 17.6% retrotransposons, 1.2% DNA transposons, and 1.4% simple repeats. De novo identification of repeats found 55.6% retrotransposons, 2.6% DNA transposons, and 8.1% unknown repeats. In total, 80.9% of the genome is masked with repetitive elements. The gene calling pipeline has generated 30, 000 reliable protein- coding gene models.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Interdisciplinarne prirodne znanosti, Šumarstvo

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