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Pregled bibliografske jedinice broj: 1219872

A chromosome-level genome assembly of Chouardia litardierei (Hyacinthaceae), a plant characterized by extreme ecological plasticity


Šarančić, Sara Laura; Križanović, Krešimir; Jakše, Jernej; Radosavljević, Ivan
A chromosome-level genome assembly of Chouardia litardierei (Hyacinthaceae), a plant characterized by extreme ecological plasticity // Proceedings of Genetika 2022 / Zorc, Minja ; Dovč, Peter (ur.).
Ljubljana: Genetic Society of Slovenia, Ljubljana, 2022. str. 101-101 (poster, međunarodna recenzija, sažetak, znanstveni)


CROSBI ID: 1219872 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
A chromosome-level genome assembly of Chouardia litardierei (Hyacinthaceae), a plant characterized by extreme ecological plasticity

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

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

Izvornik
Proceedings of Genetika 2022 / Zorc, Minja ; Dovč, Peter - Ljubljana : Genetic Society of Slovenia, Ljubljana, 2022, 101-101

ISBN
978-961-93545-7-5

Skup
9th Congress of the Genetic Society of Slovenia

Mjesto i datum
Ljubljana, Slovenija, 28.09.2022. - 30.09.2022

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
genome plasticity, de-novo genome assembly, Hi-C, long reads technology

Sažetak
Amethyst meadow squill (Chouardia litardierei, Hyacinthaceae) is a plant species characterized by exceptional ecological plasticity. Its populations are found in ecologically highly contrasting environments, from salt marshes near seashores, across periodically flooded karst fields, to arid mountain slopes in high altitudes. Nowadays, knowledge of the molecular mechanisms underlying the adaptive divergence and speciation processes can be gained by exploring complex interactions among environment, phenotype, epigenotype, and genotype of such a species as C. litardierei, and the availability of the species' genome sequence is an absolute prerequisite. To tackle this task, by implementing long-read PacBio sequencing followed by Hi-C scaffolding, we have obtained a high-quality assembly of the C. litardierei genome. The species is characterized by n=13 chromosomes and a large genome of an estimated size of 4.1 Gb. Pacific Bioscience HiFi technology providing longer reads of high quality was used for generating genomic sequences. In total, 6.526.182 Hi-Fi reads were obtained with a total size of 94.54 Gb and an average read length of 14.5 Kb. Reads were de-novo assembled into contigs by haplotype-resolved de novo assembler software hifiasm (v. 0.16.1-r375). Chromosomal scaffolding was obtained by high coverage Illumina Hi-C reads (1.72 billion reads, 432.3 Gb of data representing 100X coverage) using the Juicer, 3d-dna, and Juicebox scaffolding tools. The final assembly counted 13 main scaffolds, representing the expected number of chromosomes in a total length of 3, 33 Gb, while all scaffolds had a length of 3, 70 Gb. The average genome GC content has 42.9%. BUSCO analysis confirmed the high completeness of the assembly since only 2.6% of the liliopsida_odbio dataset was missing. As expected, a high proportion of various repeats in the genome was found. RepeatMasker screening against the curated libraries for Viridiplantae repeats (Dfam and Repbase) revealed 17.6% retrotransposons and 1.2% DNA transposons, while de-novo identification of repeats confirmed 55.6% retrotransposons, 2.6% DNA transposons, and 8.1% unknown repeats. The MAKER gene calling pipeline has generated 34, 000 reliable protein-coding gene models. Comparison with the complete garlic (Allium sativa L.) genome from the same order of Asparagales revealed a low level of conserved synteny.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Interdisciplinarne prirodne znanosti, Šumarstvo



POVEZANOST RADA


Projekti:
--IP-2020-02-8099 - Livadni procjepak (Chouardia litardierei, Hyacinthaceae) kao istraživački sustav ekološke divergencije (AMS-EcolDiv) (Radosavljević, Ivan) ( CroRIS)


Citiraj ovu publikaciju:

Šarančić, Sara Laura; Križanović, Krešimir; Jakše, Jernej; Radosavljević, Ivan
A chromosome-level genome assembly of Chouardia litardierei (Hyacinthaceae), a plant characterized by extreme ecological plasticity // Proceedings of Genetika 2022 / Zorc, Minja ; Dovč, Peter (ur.).
Ljubljana: Genetic Society of Slovenia, Ljubljana, 2022. str. 101-101 (poster, međunarodna recenzija, sažetak, znanstveni)
Šarančić, S., Križanović, K., Jakše, J. & Radosavljević, I. (2022) A chromosome-level genome assembly of Chouardia litardierei (Hyacinthaceae), a plant characterized by extreme ecological plasticity. U: Zorc, M. & Dovč, P. (ur.)Proceedings of Genetika 2022.
@article{article, author = {\v{S}aran\v{c}i\'{c}, Sara Laura and Kri\v{z}anovi\'{c}, Kre\v{s}imir and Jak\v{s}e, Jernej and Radosavljevi\'{c}, Ivan}, year = {2022}, pages = {101-101}, keywords = {genome plasticity, de-novo genome assembly, Hi-C, long reads technology}, isbn = {978-961-93545-7-5}, title = {A chromosome-level genome assembly of Chouardia litardierei (Hyacinthaceae), a plant characterized by extreme ecological plasticity}, keyword = {genome plasticity, de-novo genome assembly, Hi-C, long reads technology}, publisher = {Genetic Society of Slovenia, Ljubljana}, publisherplace = {Ljubljana, Slovenija} }
@article{article, author = {\v{S}aran\v{c}i\'{c}, Sara Laura and Kri\v{z}anovi\'{c}, Kre\v{s}imir and Jak\v{s}e, Jernej and Radosavljevi\'{c}, Ivan}, year = {2022}, pages = {101-101}, keywords = {genome plasticity, de-novo genome assembly, Hi-C, long reads technology}, isbn = {978-961-93545-7-5}, title = {A chromosome-level genome assembly of Chouardia litardierei (Hyacinthaceae), a plant characterized by extreme ecological plasticity}, keyword = {genome plasticity, de-novo genome assembly, Hi-C, long reads technology}, publisher = {Genetic Society of Slovenia, Ljubljana}, publisherplace = {Ljubljana, Slovenija} }




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