Abstract
Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these “classical” maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that were identified by morphological phenotype prior to cloning, are retained at syntenic locations throughout the grasses at much higher levels than the average expressed maize gene, and are preferentially found on the maize1 subgenome even with a duplicate copy is still retained on the opposite subgenome. Maize1 is the subgenome that experienced less gene loss following the whole genome duplication in maize lineage 5–12 million years ago and genes located on this subgenome tend to be expressed at higher levels in modern maize. Links to the web based software that supported our syntenic analyses in the grasses should empower further research and support teaching involving the history of maize genetic research. Our findings exemplify the concept of “grasses as a single genetic system,” where what is learned in one grass may be applied to another.
Highlights
The grasses, the approximately 10,000 species in the family Poaceae, are one of the most ecologically and economically significant taxa on the planet
Comparative mapping of diverse grass species led to the conclusion that they are all similar in gene content and order [1,2] to the point that it was argued grasses could be treated as a single genetic system, sharing map data, markers, and leveraging inter-specific hybrids to dissect the genes responsible for morphological variation between different grass lineages [3]
Aside from missed UTR exons and the genes which were classified as supported only by ab initio prediction despite being supported by sequences in GenBank, the most frequent error we identified were genes that had been split into multiple unlinked gene models by maizesequence.org
Summary
The grasses, the approximately 10,000 species in the family Poaceae, are one of the most ecologically and economically significant taxa on the planet. Knowledge gained from the study of any one grass species could be quickly and directly applied to all other species in the family. Maize is without question the species with the longest and most comprehensively documented history of genetic investigation. The rich genetic resources found in maize are the result of over a century of genetic investigation beginning with R. A. Emerson’s small but distinguished group in the early 20th century; see B. The resulting set of characterized genes has the potential to be of great value in the genomics era and sets maize apart from many model systems of more recent origin. Until now the applications of this information in a genomic context have been severely limited by the lack of reliable connections between the data produced by geneticists studying individual genes and the datasets produced by genomicists who generally work at the level of whole genomes
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