Genomic abundance is not predictive of tandem repeat localization in grass genomes.

Highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Previous research has investigated variation in centromere repeats across eukaryotes, positing that the highest abundance tandem repeat in a genome is often the centromeric repeat. To test this assumption, we used shotgun sequencing and a bioinformatic pipeline to identify common tandem repeats across a number of grass species. We find that de novo assembly and subsequent abundance ranking of repeats can successfully identify tandem repeats with homology to known tandem repeats. Fluorescent in-situ hybridization shows that de novo assembly and ranking of repeats from non-model taxa identifies chromosome domains rich in tandem repeats both near pericentromeres and elsewhere in the genome

Genomic abundance is not predictive of tandem repeat localization in grass genomes.

Highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Previous research has investigated variation in centromere repeats across eukaryotes, positing that the highest abundance tandem repeat in a genome is often the centromeric repeat. To test this assumption, we used shotgun sequencing and a bioinformatic pipeline to identify common tandem repeats across a number of grass species. We find that de novo assembly and subsequent abundance ranking of repeats can successfully identify tandem repeats with homology to known tandem repeats. Fluorescent in-situ hybridization shows that de novo assembly and ranking of repeats from non-model taxa identifies chromosome domains rich in tandem repeats both near pericentromeres and elsewhere in the genome

Data from: Allopolyploidy, diversification, and the Miocene grassland expansion

The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high frequency of polyploids. A phylogeny was constructed for ca. 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C4 grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum. We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation

Counts of reads per sequence library for each taxa.

<p>An accession ID of NA indicates a purchase from a local nursery or sample not registered with GRIN. Taxa were selected broadly from across the Andropogoneae tribe, with higher density sampling in the <i>Tripsacum</i> genus to study tandem repeat variation within a genus. We used <i>A. nepalensis</i>, rice, and bamboo as outgroups to the Andropogoneae. Asterisks indicate genome size estimates published in this study. GS = Genome size.</p

Fluorescent in situ hybridization of the highest abundant tandem repeats in three grasses.

<p>(A1-C1) Somatic metaphase chromosomes prepared from <i>A. nepalensis</i> (A1), <i>H. hirta</i> (B1), and <i>U. digitatum</i> (C1), respectively. (A2-C2) FISH signals derived from the three repeats identified in the three species. (A3-C3) Images merged from chromosomes and FISH signals. Scale bar = 10 microns. On all images, knobs are indicated with white arrows.</p

Genomic composition of top 4 tandemly repetitive contigs.

<p>The top 4 contigs in each species were defined as not having homology to one another, in order to identify independent repeat motifs. Species are ordered in approximate phylogenetic relationship, with a phylogenetic schematic below the graph. Values were calculated as a percentage of total genomic reads mapping to each tandem repeat family. Tandem repeat families are ordered by their genomic abundance from left to right.</p

Percentage genomic composition of all tandem repeat contigs in monocot taxa.

<p>Values are derived from the proportion of all reads mapping to any tandemly repetitive contig derived from TRF after MIRA assembly. Species are ordered in approximate phylogenetic relationship, with a phylogenetic schematic below the graph.</p

Alignments of Orthologous and Paralogous Isolates for Allopolyploidy Identification in Andropogoneae

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Uneven chromosome contraction and expansion in the maize genome

Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive duplicated regions within its genome. We have sequenced the two copies of one such region, generating 7.8 Mb of sequence spanning 17.4 cM of the short arm of chromosome 1 and 6.6 Mb (25.6 cM) from the long arm of chromosome 9. Rice, which did not undergo a similar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome 3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowed identification of syntenic blocks, and indicated that the maize regions have undergone differential contraction in genic and intergenic regions and expansion by the insertion of retrotransposable elements. Approximately 9% of the predicted genes in each duplicated region are completely missing in the rice genome, and almost 20% have moved to other genomic locations. Predicted genes within these regions tend to be larger in maize than in rice, primarily because of the presence of predicted genes in maize with larger introns. Interestingly, the general gene methylation patterns in the maize homoeologous regions do not appear to have changed with contraction or expansion of their chromosomes. In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species