Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another

Whole exome sequencing identifies recessive PKHD1 mutations in a Chinese twin family with Caroli disease.

BACKGROUND: Mutations in PKHD1 cause autosomal recessive Caroli disease, which is a rare congenital disorder involving cystic dilatation of the intrahepatic bile ducts. However, the mutational spectrum of PKHD1 and the phenotype-genotype correlations have not yet been fully established. METHODS: Whole exome sequencing (WES) was performed on one twin sample with Caroli disease from a Chinese family from Shandong province. Routine Sanger sequencing was used to validate the WES and to carry out segregation studies. We also described the PKHD1 mutation associated with the genotype-phenotype of this twin. RESULTS: A combination of WES and Sanger sequencing revealed the genetic defect to be a novel compound heterozygous genotype in PKHD1, including the missense mutation c.2507 T>C, predicted to cause a valine to alanine substitution at codon 836 (c.2507T>C, p.Val836Ala), and the nonsense mutation c.2341C>T, which is predicted to result in an arginine to stop codon at codon 781 (c.2341C>T, p.Arg781*). This compound heterozygous genotype co-segregates with the Caroli disease-affected pedigree members, but is absent in 200 normal chromosomes. CONCLUSIONS: Our findings indicate exome sequencing can be useful in the diagnosis of Caroli disease patients and associate a compound heterozygous genotype in PKHD1 with Caroli disease, which further increases our understanding of the mutation spectrum of PKHD1 in association with Caroli disease

Selective Catalytic Reduction of Nitric Oxide with Propylene over Fe/Beta Catalysts Under Lean-Burn Conditions

Fe/Beta catalysts were used for the selective catalytic reduction of nitric oxide with propylene (C3H6-SCR) under lean-burn conditions, which were prepared by liquid ion-exchange (LIE), solid-state ion-exchange (SIE), and incipient wet-impregnation (IWI) methods. The iron species on Fe/Beta were characterized and identified by a combination of several characterization techniques. The results showed preparation methods had a significant influence on the composition and distribution of iron species, LIE method inclined to produce more isolated Fe3+ ions at ion-exchanged sites than IWI and SIE method. C3H6-SCR activity tests demonstrated Fe/Beta(LIE) possessed remarkable catalytic activity and N2 selectivity at temperature 300⁻450 °C. Kinetic studies of C3H6-SCR reaction suggested that isolated Fe3+ species were more active for NO reduction, whereas Fe2O3 nanoparticles enhanced the hydrocarbon combustion in excess of oxygen. According to the results of in situ DRIFTS, more isolated Fe3+ sites on Fe/Beta(LIE) would promote the formation of the key intermediates, i.e., NO2 adspecies and formate species, then led to the superior C3H6-SCR activity. The slight decrease of SCR activity after hydrothermal aging of Fe/Beta(LIE) catalyst might be due to the migration of isolated Fe3+ ions into oligomeric clusters and/or Fe2O3 nanoparticles

Effects of Biological Nitrogen Metabolism on Glufosinate-Susceptible and -Resistant Goosegrass (<i>Eleusine indica</i> L.)

Glufosinate is a broad-spectrum herbicide used to control most weeds in agriculture worldwide. Goosegrass (Eleusine indica L.) is one of the top ten malignant weeds across the world, showing high tolerance to glufosinate via different mechanisms that are not yet fully understood. This study revealed that nitrogen metabolism could be a target-resistant site, providing clues to finally clarify the mechanism of glufosinate resistance in resistant goosegrass populations. Compared to susceptible goosegrass (NX), the resistant goosegrass (AUS and CS) regarding the stress of glufosinate showed stronger resistance with lower ammonia contents, higher target enzyme GS (glutamine synthetase) activity, and lower GOGAT (glutamine 2-oxoglutarate aminotransferase) activity. The GDH (glutamate dehydrogenase) activity of another pathway increased, but its gene expression was downregulated in resistant goosegrass (AUS). Analyzing the transcriptome and proteome data of goosegrass under glufosinate stress at 36 h showed that the KEGG pathway of the nitrogen metabolism was enriched in glufosinate-susceptible goosegrass (NX), but not in glufosinate-resistant goosegrass (CS and AUS). Several putative target genes involved in glufosinate stress countermeasures were identified. This study provides specific insights into the nitrogen metabolism of resistant goosegrass, and gives a basis for future functional verification of glufosinate-tolerance genes in plants

Partial sequence of exon 24 in the <i>PKHD1</i> from member of this Caroli disease-affected pedigree.

<p>(b), (c) and (d) Arrowhead indicates the heterozygous T and C at nucleotide 2507 in proband, elder twins and their father respectively. (a) Arrowhead indicates the T at nucleotide 2507 (wild type) in their mother.</p

Multiple-sequence alignment of the PKHD1 protein including <i>Mus musculus</i>, <i>Rattus norvegicus</i>, <i>Pan paniscus</i>, <i>Xenopus (Silurana) tropicalis</i>, <i>Falco cherrug</i>, <i>Zonotrichia albicollis</i> and <i>Homo sapiens</i>.

<p>The Val 836 residue is located within a highly conserved region.</p

Metabolomics Characterization of Scleractinia Corals with Different Life-History Strategies: A Case Study about Pocillopora meandrina and Seriatopora hystrix in the South China Sea

Life-history strategies play a critical role in susceptibility to environmental stresses for Scleractinia coral. Metabolomics, which is capable of determining the metabolic responses of biological systems to genetic and environmental changes, is competent for the characterization of species&rsquo; biological traits. In this study, two coral species (Pocillopora meandrina and Seriatopora hystrix in the South China Sea) with different life-history strategies (&ldquo;competitive&rdquo; and &ldquo;weedy&rdquo;) were targeted, and untargeted mass spectrometry metabolomics combined with molecular networking was applied to characterize their differential metabolic pathways. The results show that lyso-platelet activating factors (lyso-PAFs), diacylglyceryl carboxyhydroxymethylcholine (DGCC), aromatic amino acids, and sulfhydryl compounds were more enriched in P. meandrina, whereas new phospholipids, dehydrated phosphoglycerol dihydroceramide (de-PG DHC), monoacylglycerol (MAG), fatty acids (FA) (C &lt; 18), short peptides, and guanidine compounds were more enriched in S. hystrix. The metabolic pathways involved immune response, energy metabolism, cellular membrane structure regulation, oxidative stress system, secondary metabolite synthesis, etc. While the immune system (lysoPAF) and secondary metabolite synthesis (aromatic amino acids and sulfhydryl compounds) facilitates fast growth and resistance to environmental stressors of P. meandrina, the cell membrane structure (structural lipids), energy storage (storage lipids), oxidative stress system (short peptides), and secondary metabolite synthesis (guanidine compounds) are beneficial to the survival of S. hystrix in harsh conditions. This study contributes to the understanding of the potential molecular traits underlying life-history strategies of different coral species