Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time

Abstract

Tandem duplicate genes are proximally duplicated and as such occur in similar genomic neighborhoods. Using the maize B73 and PH207 de novo genome assemblies, we identified thousands of tandem gene duplicates that account for ∼10% of the annotated genes. These tandem duplicates have a bimodal distribution of ages, which coincide with ancient allopolyploidization and more recent domestication. Tandem duplicates are smaller on average and have a higher probability of containing LTR elements than other genes, suggesting origins in nonhomologous recombination. Within relatively recent tandem duplicate genes, ∼26% appear to be undergoing degeneration or divergence in function from the ancestral copy. Our results show that tandem duplicates are abundant in maize, arose in bursts throughout maize evolutionary history under multiple potential mechanisms, and may provide a substrate for novel phenotypic variation.

Evolution of the RNA N6-Methyladenosine Methylome Mediated by Genomic Duplication

“…The coevolution between m 6 A genes and TEs was also exemplified by evolutionary analysis of TD genes methylated by m 6 A. In total, we obtained 4,448 TD genes from 1,758 TD clusters identified by Kono et al (2018). We observed that both K a and K s values of m 6 A and non-m 6 A TD genes are significantly higher than those of non-TD genes.…”

“…Then, the subgenome identity of each maize chromosome was determined using a previously described method (Schnable et al, 2011). The maize tandem duplicate genes in our study were obtained from Kono et al (2018). The coding sequences of homologous gene pairs were aligned using the MAFFT v7.271 software (Katoh and Standley, 2013).…”

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

“…For example, this mechanism has been shown to confer soybean resistance against cyst nematode ( Heterodera glycines ) at Rhg1 , a quantitative trait locus on chromosome 18, by changing the copy number variation that increases the gene expression [ 33 ]. In maize, thousands of tandem gene duplicates were identified that correspond to about 10% of the annotated genes [ 34 ]. Some of them may contribute to a phenotypic variation such as the White Cap locus , which provided the possibility to select white-grain color [ 35 ].…”

Extensive genome-wide duplications in the eastern oyster (Crassostrea virginica)

“…In agriculturally important species (e.g. maize and cattle), breed-specific CNVs can affect complex traits and may be valuable in informing future breeding strategies [24,25]. Studies in non-model organisms, including plants, fish and mammals, have found high levels of standing variation in CNVs [26–30].…”