Management of University Biological Collections: A Framework for Policy and Practice

A broad-based task force, chaired by Lynn Kimsey of the Department of Entomology and director of the Bohart Entomological Museum, was convened to review and assess the status of living and preserved biological collections held on the Davis campus of the University of California. The task force addressed three basic issues, forming subcommittees to 1) review the data gathered in a survey by the Genetic Resources Conservation Program of living and preserved collections and report its findings, 2) make recommendations for policy guidelines on a campus basis and an individual-collection basis, and s) propose a campus-wide administrative structure to address issues of communication, documentation, and funding. Policy for administration, ownership, transfer, and disposal of collections has apparently not been previously addressed by the University of California. The task force\u27s recommendations on policy and administrative issues are the subject of this report

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials.

BackgroundMutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis.ResultsWe first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number.ConclusionSlow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials

Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B.

Key messageComparison of genome sequences of wild emmer wheat and Aegilops tauschii suggests a novel scenario of the evolution of rearranged wheat chromosomes 4A, 5A, and 7B. Past research suggested that wheat chromosome 4A was subjected to a reciprocal translocation T(4AL;5AL)1 that occurred in the diploid progenitor of the wheat A subgenome and to three major rearrangements that occurred in polyploid wheat: pericentric inversion Inv(4AS;4AL)1, paracentric inversion Inv(4AL;4AL)1, and reciprocal translocation T(4AL;7BS)1. Gene collinearity along the pseudomolecules of tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, subgenomes AABB) and diploid Aegilops tauschii (genomes DD) was employed to confirm these rearrangements and to analyze the breakpoints. The exchange of distal regions of chromosome arms 4AS and 4AL due to pericentric inversion Inv(4AS;4AL)1 was detected, and breakpoints were validated with an optical Bionano genome map. Both breakpoints contained satellite DNA. The breakpoints of reciprocal translocation T(4AL;7BS)1 were also found. However, the breakpoints that generated paracentric inversion Inv(4AL;4AL)1 appeared to be collocated with the 4AL breakpoints that had produced Inv(4AS;4AL)1 and T(4AL;7BS)1. Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 either originated sequentially, and Inv(4AL;4AL)1 was produced by recurrent chromosome breaks at the same breakpoints that generated Inv(4AS;4AL)1 and T(4AL;7BS)1, or Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 originated simultaneously. We prefer the latter hypothesis since it makes fewer assumptions about the sequence of events that produced these chromosome rearrangements

Seasonal H2O and CO2 Ice Cycles at the Mars Phoenix Landing Site: 1. Prelanding CRISM and HiRISE Observations

The condensation, evolution, and sublimation of seasonal water and carbon dioxide ices were characterized at the Mars Phoenix landing site from Martian northern midsummer to midspring (Ls ∼ 142° – Ls ∼ 60°) for the year prior to the Phoenix landing on 25 May 2008. Ice relative abundances and grain sizes were estimated using data from the Compact Reconnaissance Imaging Spectrometer for Mars and High Resolution Imaging Science Experiment aboard Mars Reconnaissance Orbiter and a nonlinear mixing model. Water ice first appeared at the Phoenix landing site during the afternoon in late summer (Ls ∼ 167°) as an optically thin layer on top of soil. CO2 ice appeared after the fall equinox. By late winter (Ls ∼ 344°), the site was covered by relatively pure CO2 ice (∼30 cm thick), with a small amount of ∼100 μm diameter water ice and soil. As spring progressed, CO2 ice grain sizes gradually decreased, a change interpreted to result from granulation during sublimation losses. The combined effect of CO2 sublimation and decreasing H2O ice grain sizes allowed H2O ice to dominate spectra during the spring and significantly brightened the surface. CO2 ice disappeared by early spring (Ls ∼ 34°) and H2O ice by midspring (Ls ∼ 59°). Spring defrosting was not uniform and occurred more rapidly over the centers of polygons and geomorphic units with relatively higher thermal inertia values

Seasonal H2O and CO2 Ice Cycles at the Mars Phoenix Landing Site: 1. Prelanding CRISM and HiRISE Observations

The condensation, evolution, and sublimation of seasonal water and carbon dioxide ices were characterized at the Mars Phoenix landing site from Martian northern midsummer to midspring (Ls ∼ 142° – Ls ∼ 60°) for the year prior to the Phoenix landing on 25 May 2008. Ice relative abundances and grain sizes were estimated using data from the Compact Reconnaissance Imaging Spectrometer for Mars and High Resolution Imaging Science Experiment aboard Mars Reconnaissance Orbiter and a nonlinear mixing model. Water ice first appeared at the Phoenix landing site during the afternoon in late summer (Ls ∼ 167°) as an optically thin layer on top of soil. CO2 ice appeared after the fall equinox. By late winter (Ls ∼ 344°), the site was covered by relatively pure CO2 ice (∼30 cm thick), with a small amount of ∼100 μm diameter water ice and soil. As spring progressed, CO2 ice grain sizes gradually decreased, a change interpreted to result from granulation during sublimation losses. The combined effect of CO2 sublimation and decreasing H2O ice grain sizes allowed H2O ice to dominate spectra during the spring and significantly brightened the surface. CO2 ice disappeared by early spring (Ls ∼ 34°) and H2O ice by midspring (Ls ∼ 59°). Spring defrosting was not uniform and occurred more rapidly over the centers of polygons and geomorphic units with relatively higher thermal inertia values

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

<p>Abstract</p> <p>Background</p> <p>Many plants have large and complex genomes with an abundance of repeated sequences. Many plants are also polyploid. Both of these attributes typify the genome architecture in the tribe Triticeae, whose members include economically important wheat, rye and barley. Large genome sizes, an abundance of repeated sequences, and polyploidy present challenges to genome-wide SNP discovery using next-generation sequencing (NGS) of total genomic DNA by making alignment and clustering of short reads generated by the NGS platforms difficult, particularly in the absence of a reference genome sequence.</p> <p>Results</p> <p>An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions from repetitive sequences and sequences shared by paralogous genes. Multiple genome equivalents of shotgun reads of another genotype generated with SOLiD or Solexa are then mapped to the annotated Roche 454 reads to identify putative SNPs. A pipeline program package, AGSNP, was developed and used for genome-wide SNP discovery in <it>Aegilops tauschii-</it>the diploid source of the wheat D genome, and with a genome size of 4.02 Gb, of which 90% is repetitive sequences. Genomic DNA of <it>Ae. tauschii </it>accession AL8/78 was sequenced with the Roche 454 NGS platform. Genomic DNA and cDNA of <it>Ae. tauschii </it>accession AS75 was sequenced primarily with SOLiD, although some Solexa and Roche 454 genomic sequences were also generated. A total of 195,631 putative SNPs were discovered in gene sequences, 155,580 putative SNPs were discovered in uncharacterized single-copy regions, and another 145,907 putative SNPs were discovered in repeat junctions. These SNPs were dispersed across the entire <it>Ae. tauschii </it>genome. To assess the false positive SNP discovery rate, DNA containing putative SNPs was amplified by PCR from AL8/78 and AS75 and resequenced with the ABI 3730 xl. In a sample of 302 randomly selected putative SNPs, 84.0% in gene regions, 88.0% in repeat junctions, and 81.3% in uncharacterized regions were validated.</p> <p>Conclusion</p> <p>An annotation-based genome-wide SNP discovery pipeline for NGS platforms was developed. The pipeline is suitable for SNP discovery in genomic libraries of complex genomes and does not require a reference genome sequence. The pipeline is applicable to all current NGS platforms, provided that at least one such platform generates relatively long reads. The pipeline package, AGSNP, and the discovered 497,118 <it>Ae. tauschii </it>SNPs can be accessed at (<url>http://avena.pw.usda.gov/wheatD/agsnp.shtml</url>).</p

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms

Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

<p>Abstract</p> <p>Background</p> <p>The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy.</p> <p>Results</p> <p>The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an <it>in silico </it>merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries.</p> <p>Conclusions</p> <p>The negligibly low level of incorporation of clones from homoeologous chromosome arms into a contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes.</p