The Stromal Processing Peptidase of Chloroplasts is Essential in Arabidopsis, with Knockout Mutations Causing Embryo Arrest after the 16-Cell Stage

Stromal processing peptidase (SPP) is a metalloendopeptidase located in the stroma of chloroplasts, and it is responsible for the cleavage of transit peptides from preproteins upon their import into the organelle. Two independent mutant Arabidopsis lines with T-DNA insertions in the SPP gene were analysed (spp-1 and spp-2). For both lines, no homozygous mutant plants could be detected, and the segregating progeny of spp heterozygotes contained heterozygous and wild-type plants in a ratio of 2∶1. The siliques of heterozygous spp-1 and spp-2 plants contained many aborted seeds, at a frequency of ∼25%, suggesting embryo lethality. By contrast, transmission of the spp mutations through the male and female gametes was found to be normal, and so gametophytic effects could be ruled out. To further elucidate the timing of the developmental arrest, mutant and wild-type seeds were cleared and analysed by Nomarski microscopy. A significant proportion (∼25%) of the seeds in mutant siliques exhibited delayed embryogenesis compared to those in wild type. Moreover, the mutant embryos never progressed normally beyond the 16-cell stage, with cell divisions not completing properly thereafter. Heterozygous spp mutant plants were phenotypically indistinguishable from the wild type, indicating that the spp knockout mutations are completely recessive and suggesting that one copy of the SPP gene is able to produce sufficient SPP protein for normal development under standard growth conditions

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop

Ultrasonography of the rumen of dairy cows

Background This study describes the ultrasonographic findings of the rumen in 45 healthy dairy cows. Results The cows were scanned on both sides using a 5.0 MHz transducer. The dorsal visible margin of the rumen ran parallel to the lung from cranioventral to caudodorsal. It was furthest from the dorsal midline at the 9th intercostal space (48.3 ± 9.24 cm) and closest at the 12th intercostal space (22.4 ± 3.27 cm). The longitudinal groove, which could be clearly identified at all examination sites because it appeared as a triangular notch, formed the ventral margin of the dorsal sac of the rumen. The dorsal sac of the rumen was largest at the caudal flank (40.3 ± 6.33 cm), where it was adjacent to the abdominal wall. The ventral sac of the rumen extended across the ventral midline into the right hemiabdomen and its ventral margin had a largely horizontal craniocaudal course. The height of the ventral sac of the rumen exceeded that of the dorsal sac at all examination sites; the maximum height was measured at the 12th intercostal space (62.6 ± 9.53 cm). The dorsal gas cap, characterised ultrasonographically by typical reverberation artifacts, was visible in all cows from the 12th intercostal space to the caudal flank. It was largest at the 12th intercostal space (20.5 ± 7.03 cm). The transition from the gas cap to the fibre mat was marked by the abrupt cessation of the reverberation artifacts. It was not possible to differentiate a fibre mat and a ventral fluid phase. The rumen could be imaged from the right side in 21 cows (47%). Conclusions Ultrasonography is well suited for the detailed examination of the rumen of cows. The reference values obtained from this study add to the diagnostic tools that are available for the assessment of bovine patients

Control of PHERES1 Imprinting in Arabidopsis by Direct Tandem Repeats

ABSTRACT Genomic imprinting is an epigenetic phenomenon that causes monoallelic expression of specific genes dependent on the parent-of-origin. Imprinting of the Arabidopsis gene PHERES1 requires the function of the FERTILIZATION INDEPENDENT SEED (FIS) Polycomb group complex as well as a distally located methylated region containing a tandem triple repeat sequence. In this study, we investigated the regulation of the close PHERES1 homolog PHERES2. We found that PHERES2 is also a direct target gene of the FIS Polycomb group complex, but, in contrast to PHERES1, PHERES2 is equally expressed from maternal and paternal alleles. Thus, PHERES2 is not regulated by genomic imprinting, correlating with the lack of tandem repeats at PHERES2. Eliminating tandem repeats from the PHERES1 locus abolishes PHERES1 imprinting, demonstrating that tandem repeats are essential for PHERES1 imprinting. Taking these results together, our study shows that the recently duplicated genes PHERES1 and PHERES2 are both target genes of the FIS Polycomb group complex but only PHERES1 is regulated by genomic imprinting, which is likely caused by the presence of repeat sequences in the proximity of the PHERES1 locus