Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.

No abstract

Re-domestication of potato into an inbred line-based diploid crop propagated by seed represents a promising alternative to traditional clonal propagation of tetraploid potato, but self-incompatibility has hindered the development of inbred lines. To address this problem, we created self-compatible diploid potatoes by knocking out the self-incompatibility gene S-RNase using the CRISPR-Cas9 system. This strategy opens new avenues for diploid potato breeding and will also be useful for studying other self-incompatible crops.

No abstract

We report two NMR complex structures of PHD UHRF1 binding to unmodified or K9 trimethylated histone tails, which clarify a controversy regarding how the binding of UHRF1 to H3 tails is mediated. Based on our structures, H3R2, not H3K9, mediates PHD binding.Human UHRF1, also known as ICBP90, plays central roles in maintaining CpG DNA methylation [1,2] and epigenetic code inheritance [3]. It harbors five recognizable functional domains: an ubiquitin-like domain (UBL) at the N-terminus, a tandem tudor domain (Tudor UHRF1 ), a plant homeodomain (PHD UHRF1 ), a SET and RING associated (SRA) domain and a RING domain at the C-terminus, which mediate interactions of UHRF1 with histones and DNA ( Figure 1A). Previous studies suggested that PHD UHRF1 defines binding specificity of UHRF1 to trimethylated H3 tail H3K9me3 [3]. However, recent studies showed that H3K9me3 binding is mediated by the Tudor UHRF1 [4,5]. PHD UHRF1 is structurally different from the canonical PHD fingers (Figure 1). It has additional Cys residues at its amino terminal portion; it is also devoid of the residues to form the H3K4me3-binding aromatic cage [6][7][8][9] and a terminal aspartic acid residue to recognize H3K4me0 [10][11][12][13]. Therefore, exactly how PH-D UHRF1 binds to the N-terminal H3 tail remains unclear.To address this issue, we determined 3D NMR structures of free PHD UHRF1 , and two complexes, namely PH-D UHRF1 -H3K9me0 and PHD UHRF1 -H3K9me3 (Figure 1 and Supplementary information, Data S1, Figure S1, Table S2). In these three structures, PHD UHRF1 is coordinated by three zinc ions to form a rod-shape structure, containing a small α-helix, a double-stranded anti-parallel β-sheet and three loops. The free and bound PHD UHRF1 structures have backbone atoms RMSD value of 1.7 Å, indicating that H3 peptides binding does not induce overall major conformational changes of PHD UHRF1 . The C-terminus of PHD UHRF1 is coordinated by two zinc ions in an interleaved, compact manner, which is similar to the reported histone tail-binding PHD domain structures (Figure 1) [6][7][8][9][10][11][12][13]. However, a difference lies at the N-terminus of In both structures of PHD UHRF1 -H3K9me0 and PH-D UHRF1 -H3K9me3 ( Figure 1B-1E), the N terminus of H3 peptide is anchored through nonpolar interactions between methyl group of H3A1 and hydrophobic side chains of PHD UHRF1 residues L344, P366 and W371 and hydrogen bonds between H3A1 nitrogen atom and backbone oxygen of PHD UHRF1 P366 and D369. Apparently, H3 residues R8 and K9 (unmethylated or trimethylated) have no interaction with PHD UHRF1 , with their sidechains extending outwards. Recently, it was reported that H3K9me3 is recognized via tandem Tudor domain [4,5], this may explain why the side chain of H3K9 does not make contact with PHD UHRF1 in our complex structures. The first zinc finger almost has no contact with histone peptides ( Figure 1B-1E), except that backbone oxygen atom of PHD UHRF1 C329 forms a hydrogen bond with the side-chain nitrogen atom (Nξ) of H3K4. The second zinc finger seem...

No abstract

Background: Vps4 ATPase is stimulated by the interaction between Vta1 and Vps60, but the structural basis for this interaction remains unclear. Results: The structure of the Vta1 N-terminal domain (Vta1NTD) in complex with Vps60(128 -186) was determined. Conclusion: Vps60(128 -186) interacts with Vta1NTD through helices ␣4Ј and ␣5Ј, extending over Vta1NTD MIT2 domain helices 1-3. Significance: This is a novel MIT recognition mode.

Hexagonal β-NaYF4 was synthesized as capped bipyramidal microdisks solvothermally from yttria (Y2O3), sodium fluoride and ammonium hydrogen fluoride. The microdisks are bound by up to eighteen faces; six {202̅3} facets on both the top and bottom of the disk and six radial {101̅0} facets around its central band. The overall morphology and particle size can be modified through change of temperature or alcoholic solvent, both of which affect the development of the {101̅0} faces. The photoluminescence properties of doped microdisks, such as down-conversion in the case of β-NaYF4:Eu3+ or up-conversion for β-NaYF4:Yb3+/Er3+, were investigated in detail. The lifetime and emission of the Eu3+ and Er3+ ions appear related to the morphology of the host crystals. This system provides an excellent example in the tuning and optimization of the optical properties of a material through morphological control via facile change of synthetic conditions.