Insights into the Maize Pan-Genome and Pan-Transcriptome  

Abstract

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

“…Increasing the sample size may also add to the dispensable genome, which is characterized by greater variation than the core genome and is potentially involved in environmental adaptation and organismal interactions 46 . Approximately 20% of the G. soja sequences and 51.4% of gene families were found to be dispensable, an interesting juxtaposition to the recently published pan-transcriptome of 503 maize samples where 82.7% of the representative transcript assemblies were dispensable 47 , supporting the prediction that an outbred species such as maize would have a larger dispensable genome than an autogamous species 45 .…”

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

“…The PAV states of these two genes on the genome level also showed a significant relationship with the metabolic traits mentioned above. These results show that the dispensable novel expressed sequences were important both in morphological adaptation processes as previously reported (Hirsch et al 2014), and in cellular metabolome and transcriptome regulation.…”

“…Second, the novel sequences were compared with 8,681 novel representative transcripts from whole seedling RNA-seq on a panel of 503 diverse maize inbred lines (Hirsch et al 2014). Nearly 60% (1,380 among 2,355) of the novel sequences identified in the present study had above 85% identity in the alignment with novel transcripts detected from seedling tissue (Table S6).…”

“…The construction of the maize pan-transcriptome is especially useful for the discovery of functional dispensable genes. Recently, the maize pan-transcriptome and its diversity have been studied in diverse lines (Hansey et al 2011;Hirsch et al 2014), however, we still lack knowledge about many dispensable gene function at the genome-wide level.…”

Correction

“…However, it should be complemented by information from other barley plants that have different genetic make-ups (genotypes). It is estimated that a single genotype of a given plant species contains only about 85% of all the genes present in the species as a whole 7,8 . To optimize breeding potential, more genotypes must be sequenced at high quality.…”