6 research outputs found

    Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

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    Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∌1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses

    The alpha-subunit of the heterotrimeric G-protein affects jasmonate responses in Arabidopsis thaliana

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    Heterotrimeric G-proteins have been implicated in having a role in many plant signalling pathways. To understand further the role of G-proteins, a preliminary experiment was performed to assess the impact of the Gα subunit loss-of-function mutation gpa1-1 on the Arabidopsis transcriptome. The analysis indicated that the Gα subunit may play a role in response to jasmonic acid (JA). Consistent with this, Gα mutants showed a reduced response to JA in inhibition of chlorophyll accumulation and root growth, whilst Gα gain-of-function plants overexpressing Gα showed the opposite phenotype. The levels of JA and related compounds were unaffected in the gpa1-1 mutant, as was autoregulation of the Allene Oxide Synthase (AOS) gene that encodes a key enzyme for JA biosynthesis. In contrast, further analyses using Gα loss- and gain-of-function Arabidopsis lines indicated that Gα positively modulates the expression of the Vegetative Storage Protein (VSP) gene. This indicates that the Gα subunit regulates a subset of JA-regulated genes defining a branch point in this signalling pathway in Arabidopsis. Further analysis of the impact of Gα loss of function upon the JA-regulated transcriptome using Arabidopsis full genome arrays indicated that up to 29% of genes that are >2-fold regulated by JA in the wild type are misregulated in the Gα mutant. This supports the observation that a significant proportion of, but not all, JA-regulated gene expression is mediated by Gα
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