Widespread Gene Conversion in Centromere Cores

Data from maize show that centromeres strongly suppress crossing over and instead undergo frequent genetic exchange in the form of gene conversion

Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris)

Kowar T, Zakrzewski F, Macas J, et al. Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris). BMC Plant Biology. 2016;16(1): 120.Background Sugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the recently published genome sequence, due to the fact that regions with high repetitive DNA contents (e.g. satellite DNAs) are only partially included. Therefore, to fill these gaps and to gain information about the repeat composition of centromeres and heterochromatic regions, we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using antibodies against the centromere-specific histone H3 variant of sugar beet (CenH3) and the heterochromatic mark of dimethylated lysine 9 of histone H3 (H3K9me2). Results ChIP-Seq analysis revealed that active centromeres containing CenH3 consist of the satellite pBV and the Ty3-gypsy retrotransposon Beetle7, while heterochromatin marked by H3K9me2 exhibits heterogeneity in repeat composition. H3K9me2 was mainly associated with the satellite family pEV, the Ty1-copia retrotransposon family Cotzilla and the DNA transposon superfamily of the En/Spm type. In members of the section Beta within the genus Beta, immunostaining using the CenH3 antibody was successful, indicating that orthologous CenH3 proteins are present in closely related species within this section. Conclusions The identification of repetitive genome portions by ChIP-Seq experiments complemented the sugar beet reference sequence by providing insights into the repeat composition of poorly characterized CenH3-chromatin and H3K9me2-heterochromatin. Therefore, our work provides the basis for future research and application concerning the sugar beet centromere and repeat rich heterochromatic regions characterized by the presence of H3K9me2

Light nuclei with semilocal momentum-space regularized chiral interactions up to third order

We present a systematic investigation of few-nucleon systems and light nuclei using the current LENPIC interactions comprising semilocal momentum-space regularized two- and three-nucleon forces up to third chiral order (N$^2$LO). Following our earlier study utilizing the coordinate-space regularized interactions, the two low-energy constants entering the three-body force are determined from the triton binding energy and the differential cross section minimum in elastic nucleon-deuteron scattering. Predictions are made for selected observables in elastic nucleon-deuteron scattering and in the deuteron breakup reactions, for properties of the $A=3$ and $A=4$ nuclei, and for spectra of $p$-shell nuclei up to $A = 16$. A comprehensive error analysis is performed including an estimation of correlated truncation uncertainties for nuclear spectra. The obtained predictions are generally found to agree with experimental data within errors. Similar to the coordinate-space regularized chiral interactions at the same order, a systematic overbinding of heavier nuclei is observed, which sets in for $A \sim 10$ and increases with $A$.Comment: 21 pages, 13 figures, 5 tables, added referenc

Nuclear properties with semilocal momentum-space regularized chiral interactions beyond N2LON^{2}LO

We present a comprehensive investigation of few-nucleon systems as well as light and medium-mass nuclei up to $A=48$ using the current Low Energy Nuclear Physics International Collaboration two-nucleon interactions in combination with the third-order (N$^2$LO) three-nucleon forces. To address the systematic overbinding of nuclei starting from $A \sim 10$ found in our earlier study utilizing the N$^2$LO two- and three-nucleon forces, we take into account higher-order corrections to the two-nucleon potentials up through fifth order in chiral effective field theory. The resulting Hamiltonian can be completely determined using the $A=3$ binding energies and selected nucleon-deuteron cross sections as input. It is then shown to predict other nucleon-deuteron scattering observables and spectra of light $p$-shell nuclei, for which a detailed correlated truncation error analysis is performed, in agreement with experimental data. Moreover, the predicted ground state energies of nuclei in the oxygen isotopic chain from $^{14}$O to $^{26}$O as well as $^{40}$Ca and $^{48}$Ca show a remarkably good agreement with experimental values, given that the Hamiltonian is fixed completely from the $A \leq 3$ data, once the fourth-order (N$^3$LO) corrections to the two-nucleon interactions are taken into account. On the other hand, the charge radii are found to be underpredicted by $\sim 10\%$ for the oxygen isotopes and by almost $20\%$ for $^{40}$Ca and $^{48}$Ca.Comment: 20 pages, 14 figures, 8 table

Demarcation of informative chromosomes in tropical sweet corn inbred lines using microsatellite DNA markers

A study of genetic variation among 10 pairs of chromosomes extracted from 13 tropical sweet corn inbred lines, using 99 microsatellite markers, revealed a wide range of genetic diversity. Allelic richness and the number of effective alleles per chromosome ranged from 2.78 to 4.33 and 1.96 to 3.47, respectively, with respective mean values of 3.62 and 2.73. According to the Shannon's information index (I) and Nei's gene diversity coefficient (Nei), Chromosome 10 was the most informative chromosome (I = 1.311 and Nei = 0.703), while Chromosome 2 possessed the least (I = 0.762 and Nei = 0.456). Based on linkage disequilibrium (LD) measurements for loci less than 50 cM apart on the same chromosome, all loci on Chromosomes 1, 6 and 7 were in equilibrium. Even so, there was a high proportion of genetic variation in Chromosomes 4, 5, 8, 9 and 10, thereby revealing their appropriateness for use in the genetic diversity investigations among tropical sweet corn lines. Chromosome 4, with the highest number of loci in linkage disequilibrium, was considered the best for marker-phenotype association and QTL mapping, followed by Chromosomes 5, 8, 9 and 10

The B73 Maize Genome: Complexity, Diversity, and Dynamics

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize