F1 Maize Iso-Seq - Final & Intermediate files

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Variant Phasing and Haplotypic Expression from Single-molecule Sequencing in Maize

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Maize is a diploid species with very high genetic diversity. Haplotype phasing of genetic variants in maize is important for interpretation of the genome, population genetic and functional genomic analysis of allelic activity. However, due to splicing variability and sequencing length limitation, phasing at isoform level are always very challenge. Here, we developed a tool called ‘Iso-Phase’ to phase the isoforms in hybrids and present the first isoforms phasing study in maize using inbred lines B73 and Ki11, as well as their reciprocal crosses from full-length single-molecule sequencing. Our results show that maize parental lines and hybrid lines display different splicing activity, and 6,847 genes can be phased through Iso-Phase in two reciprocal hybrids using embryo, endosperm and root tissues. We identified parental origin isoforms in maize hybrids, different novel isoforms between maize parent and hybrid lines, provides measures of haplotypic expression that increase power and accuracy in studies of allelic expression. It is the first study of phased full-length isoforms in maize, as well as in plants, which provides insights about maize and plant heterosis at allele-specific full-length transcriptional level. The approach used in this study also provide important information for many other phasing studies in different species.