Widespread imprinting of transposable elements and variable genes in the maize endosperm


Autoři: Sarah N. Anderson aff001;  Peng Zhou aff002;  Kaitlin Higgins aff001;  Yaniv Brandvain aff002;  Nathan M. Springer aff002
Působiště autorů: Department of Genetics, Development, and Cell Biology; Iowa State University; Ames, Iowa, United States of America aff001;  Department of Plant and Microbial Biology; University of Minnesota; St. Paul, Minnesota, United States of America aff002
Vyšlo v časopise: Widespread imprinting of transposable elements and variable genes in the maize endosperm. PLoS Genet 17(4): e1009491. doi:10.1371/journal.pgen.1009491
Kategorie: Research Article
doi: 10.1371/journal.pgen.1009491

Souhrn

Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.

Klíčová slova:

Endosperm – Gene expression – Genome annotation – Genomic imprinting – Maize – Plant genomics – Single nucleotide polymorphisms – Transposable elements


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