The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms

Nature          Published: 24 January 2018

AbstractThe planarian Schmidtea mediterranea is an important model for stem cell research and regeneration, but adequate genome resources for this species have been lacking. Here we report a highly contiguous genome assembly of S. mediterranea, using long-read sequencing and a de novo assembler (MARVEL) enhanced for low-complexity reads. The S. mediterranea genome is highly polymorphic and repetitive, and harbours a novel class of giant retroelements. Furthermore, the genome assembly lacks a number of highly conserved genes, including critical components of the mitotic spindle assembly checkpoint, but planarians maintain checkpoint function. Our genome assembly provides a key model system resource that will be useful for studying regeneration and the evolutionary plasticity of core cell biological mechanisms.

Read the original article: https://www.nature.com/articles/nature25473

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

Nature Genetics        Published: 22 January 2018

AbstractThe sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by polycomb repressive complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys’ unique biology and evolutionary/comparative perspective.

Read the original articlehttps://www.nature.com/articles/s41588-017-0036-1#article-info

NextOmics: the FIRST officially certified service provider of Oxford Nanopore sequencing in China


NextOmics, a subsidiary of Beijing GrandOmics Biosciences, has become the first officially certified service provider of Oxford Nanopore sequencing in China. NextOmics has established the Oxford Nanopore sequencing platform since September 2017, and has finished a few dozen pilot projects so far with outstanding yield and data quality. Currently, NextOmics has eleven GridIONs and two MinIONs in operation, with more sequencers on order. Additionally, a PromethION is expected to be deployed soon by NextOmics to provide high quality and high throughput sequencing services for worldwide researchers.

NextOmics started to offer Nanopore sequencing service to Chinese and worldwide customers in 2017, and has processed different types of samples such as mammals, plants and insects. As of January 17, 2018, The NextOmics Nanopore Sequencing Center has yielded more than 2Tb qualified data within a 4-month period. In particular, NextOmics has completed the sequencing and genome assembly of over 20 plant and animal species, with significantly improved assembly quality compared to previous generation of sequencers.

NextOmics has focused on offering  professional and extraordinary genome sequencing solutions of Third Generation Sequencing (TGS)/Nanopore Sequencing, especially on areas of complex genome sequencing and assembly. At the International Conference of Plant and Animal Genomics 2018 (PAG XXVI), NextOmics released the genome skimming result of Paris japonica, the largest genome (~152Gb) in the planet earth. In the past 8 years, NextOmics has participated in over 300 genome sequencing projects and published many influential research articles, such as the first de novo near-complete genome of a Chinese individual, the first near-complete Indica rice genome, the first firefly genome, and the first Eucommia ulmoides genome. In the National Plant Biology Conference 2014 (Hefei, China), NextOmics firstly proposed the “1Mb Contig N50” slogan. Now, with the arrival of Oxford Nanopore Technology, megabase-sized  contig N50 in most species will be very common in the future.

NextOmics has established a comprehensive and cutting edge omics research center by using a variety of technologies, such as the Oxford Nanopore, optical mapping (BioNano), PacBio sequencing and 3D genome mapping. In 2018, NextOmics will leverage Nanopore Technology in areas such as direct RNA sequencing and DNA/RNA modifications. We sincerely welcome worldwide customers and collaborators to work with NextOmics and enjoy the unique advantages of long read sequencing. Let’s embrace the Nanopore era!

The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology

Plant Biotechnology Journal         Published: 22 December 2017

Abstract:Pomegranate (Punica granatum L.) has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here, we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336-Mb genome, consists of 2177 scaffolds with an N50 size of 1.7 Mb and contains 30 903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis share the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the colour formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.

Read the original article: https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12875