RT Journal Article
SR Electronic
T1 Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 654533
DO 10.1101/654533
A1 Bo Wang
A1 Elizabeth Tseng
A1 Primo Baybayan
A1 Kevin Eng
A1 Michael Regulski
A1 Yinping Jiao
A1 Liya Wang
A1 Andrew Olson
A1 Kapeel Chougule
A1 Peter Van Buren
A1 Doreen Ware
YR 2020
UL http://biorxiv.org/content/early/2020/01/15/654533.abstract
AB Haplotype phasing of genetic variants in maize is important for interpretation of the genome, population genetic analysis and functional genomic analysis of allelic activity. Accordingly, accurate methods for phasing the full-length isoforms are essential for functional genomics studies. We performed an isoform-level phasing study in maize, using two inbred lines and their reciprocal crosses, based on the single-molecule full-length cDNA sequencing. To phase and analyze the full-length transcripts between hybrids and parents, we developed a tool called IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data and identified cases of allele-specific, gene-level and isoform-level expression. Our results revealed that maize parental lines and hybrid lines exhibit different splicing activities. After phasing 6,907 genes in two reciprocal hybrids using embryo, endosperm and root tissues, we annotated the SNPs and identified large-effect genes. In addition, based on single-molecule sequencing, we identified parent-of-origin isoforms in maize hybrids, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.