Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D
Artikel i vetenskaplig tidskrift, 2018

Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of secondgeneration sequencing. Saccharomyces cerevisiae strain CEN. PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction. Assembly of the reads derived from all three technologies resulted in complete sequences for all 16 yeast chromosomes, as well as themitochondrial chromosome, in one step. Further, we identified three types of DNA methylation (5mC, 4mC and 6mA). Comparison between the reference strain S288C and strain CEN. PK113-7D identified chromosomal rearrangements against a background of similar gene content between the two strains. We identified full-length transcripts through ONT direct RNA sequencing technology. This allows for the identification of transcriptional landscapes, including untranslated regions (UTRs) (5' UTR and 3' UTR) as well as differential gene expression quantification. About 91% of the predicted transcripts could be consistently detected across biological replicates grown either on glucose or ethanol. Direct RNA sequencing identified many polyadenylated non-coding RNAs, rRNAs, telomere-RNA, long non-coding RNA and antisense RNA. This work demonstrates a strategy to obtain complete genome sequences and transcriptional landscapes that can be applied to other eukaryal organisms.

Författare

Piroon Jenjaroenpun

University of Arkansas for Medical Sciences

Thidathip Wongsurawat

University of Arkansas for Medical Sciences

Rui Pereira

Chalmers, Biologi och bioteknik, Systembiologi

Preecha Patumcharoenpol

University of Arkansas for Medical Sciences

David W. Ussery

University of Arkansas for Medical Sciences

Jens B Nielsen

Chalmers, Biologi och bioteknik, Systembiologi

Danmarks Tekniske Universitet (DTU)

Intawat Nookaew

Chalmers, Biologi och bioteknik, Systembiologi

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 46 7 e38

Ämneskategorier

Medicinsk genetik

Bioinformatik och systembiologi

Genetik

DOI

10.1093/nar/gky014

PubMed

29346625