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Pregled bibliografske jedinice broj: 882157

Genome assembly of lactic acid bacteria: the case of Lactobacillus amylovorus DSM 220531T


Žunar, Bojan; Svetec Miklenić, Marina; Nestić, Davor; Lončar, Ana; Šantek, Božidar; Svetec, Ivan-Krešimir
Genome assembly of lactic acid bacteria: the case of Lactobacillus amylovorus DSM 220531T // Abstracts of European Biotechnology Conference held in Latvia during 05–07 May 2016 / Dundar, Munis ; Gartland, Kevan ; Beccari, Tommasso ; Erdem, Yagut (ur.).
Riga: Elsevier, 2016. (poster, međunarodna recenzija, sažetak, znanstveni)


Naslov
Genome assembly of lactic acid bacteria: the case of Lactobacillus amylovorus DSM 220531T

Autori
Žunar, Bojan ; Svetec Miklenić, Marina ; Nestić, Davor ; Lončar, Ana ; Šantek, Božidar ; Svetec, Ivan-Krešimir

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

Izvornik
Abstracts of European Biotechnology Conference held in Latvia during 05–07 May 2016 / Dundar, Munis ; Gartland, Kevan ; Beccari, Tommasso ; Erdem, Yagut - Riga : Elsevier, 2016

Skup
European Biotechnology Congress 2016

Mjesto i datum
Riga, Latvija, 05-07.05.2016

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Lactobacillus amylovorus, lactic acid bacteria, whole genome sequencing, genome assembly

Sažetak
Lactic acid bacteria are a ubiquitous group of Gram-positive nonsporulating cocci and bacilli that produce lactic acid as an end product of carbohydrate fermentation. They are closely associated with our everyday life as some ferment food or have health promoting effect while others spoil food or even cause diseases. Their relevance motivated whole genome sequencing of many isolates belonging to this clade. As a result, numerous sequencing reads are publicly available but it is unclear which bioinformatics tools can organize them into high-quality genome assemblies resulting in time-consuming trial-and- error based strategies. To ameliorate this problem, we tested 13 state- of-the-art assemblers using four specialized quality control tools. Assemblers were tasked with inferring genome sequence of a representative species of lactic acid bacteria, Lactobacillus amylovorus DSM 20531T, using Illumina-generated reads. Produced genome sequences varied considerably regarding total length, continuity and accuracy. Several scaffolding and assembly merging tools were tried to improve the quality of the assemblies further but had limited success. Visualization of final stage de Bruijn graph showed that many “bulges” limit continuity while graph’s shape indicated that the genome contains small plasmid. From these insights, we derive a set of guidelines which streamline the path to a high-quality genome assembly of lactic acid bacteria.

Izvorni jezik
Engleski

Znanstvena područja
Biotehnologija



POVEZANOST RADA


Ustanove
Prehrambeno-biotehnološki fakultet, Zagreb