Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.

/pdf/sequencing-of-the-sea-lamprey-petromyzon-marinus-genome-1t18ug53u7.pdf

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the ∼90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict ∼11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during ∼350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.

Draft genome of the filarial nematode parasite Brugia malayi (Science (2007) (1756))

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

/pdf/insights-into-bilaterian-evolution-from-three-spiralian-5alwx922cf.pdf

Insights into bilaterian evolution from three spiralian genomes

WormBase ParaSite - a comprehensive resource for helminth genomics.

Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide. No vaccines are available, and treatment relies on one drug, praziquantel. Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer and as a predisposing factor for HIV/AIDS. The parasite is transmitted to humans from freshwater snails. Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease and induce squamous cell carcinoma. Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites. We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.

/pdf/whole-genome-sequence-of-schistosoma-haematobium-9vakj68y6k.pdf

Whole-genome sequence of Schistosoma haematobium

Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. Here we present a draft genomic sequence for the worm. The genome provides a global insight into the molecular architecture and host interaction of this complex metazoan pathogen, revealing that it can exploit host nutrients, neuroendocrine hormones and signalling pathways for growth, development and maturation. Having a complex nervous system and a well-developed sensory system, S. japonicum can accept stimulation of the corresponding ligands as a physiological response to different environments, such as fresh water or the tissues of its intermediate and mammalian hosts. Numerous proteases, including cercarial elastase, are implicated in mammalian skin penetration and haemoglobin
degradation. The genomic information will serve as a valuable platform to facilitate development of new interventions for schistosomiasis control.

/pdf/the-schistosoma-japonicum-genome-reveals-features-of-host-3ih560ucgp.pdf

The Schistosoma japonicum genome reveals features of host-parasite interplay

Damage characteristics and new constitutive model of sandstone under wet-dry cycles

The characteristics of expansive soil, including over consolidation, swelling-shrinkage, fissures, and strength attenuation, can cause potential hazards in road construction, which are mainly manifested as subgrade swelling-shrinkage deformation and slope collapse. Effective treatment can not only ensure long-term subgrade stability but also reduce investment costs and environmental impact. In this review, the current development status of embankment filling and cutting slope treatment technology in expansive soil areas were summarized, and the classification standards of expansive soil filler, moisture retention, and antiseepage technology were described. Then, the utility of chemical, physical, biological, and solid waste modification materials in improving the engineering characteristics of core-filled expansive soil was discussed, and the cost and technical characteristics of these modification technologies were compared and analysed. Next, the application of rigid and flexible support technology in the treatment of cutting slope collapse was analysed, and the advantages and disadvantages of rigid and flexible supports were summarized. Finally, the development direction of expansive soil subgrade treatment technology was discussed. This review includes a summary of the treatment methods of highway subgrade in expansive soil areas and can provide a technical reference for treatment methods of expansive soil subgrade.

/pdf/expansive-soil-embankment-filling-and-cutting-treatment-2z5xvnsu.pdf

Zhen Huang

Papers

The Schistosoma japonicum genome reveals features of host-parasite interplay

Damage characteristics and new constitutive model of sandstone under wet-dry cycles

Expansive Soil Embankment Filling and Cutting Treatment Technology: A Systematic Review

Study on the fatigue properties and constitutive model of siltstone under the coupled action of dry‒wet cycles and cyclic loads