The genome sequence of the colonial chordate, Botryllus schlosseri

Voskoboynik, Ayelet; Neff, Norma; Sahoo, Debashis; Newman, Aaron M.; Pushkarev, Dmitry; Koh, Winston; Passarelli, Benedetto; Fan, Hai-Wei; Mantalas, Gary L.; Palmeri, Karla J.; Ishizuka, Katherine J.; Gissi, Carmela; Griggio, Francesca; Ben‐Shlomo, Rachel; Corey, Daniel; Penland, Lolita; White, Richard Allen; Weissman, Irving L.; Quake, Stephen R.

doi:10.7554/elife.00569

Cited by 227 publications

(238 citation statements)

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“…We proposed that the ultimate extension of clonal stem cell competitions was cancer and that this limitation of fusion to kin protected both the diversity and the viability of the species (161,183,184). To follow these up in the tunicates, we determined the whole genome sequence of B. schlosseri (185) and found that the blood cell genes were most similar of all invertebrate genes to the vertebrate sequences, adding to the possibility that colonial protochrodates, likely at their tadpole stage, are the link between invertebrates and vertebrates (185) in speciation. We also cloned the histocompatibility gene, now called Botryllus histocompatibility factor (BHF), showing that a single amino acid change was sufficient to block self-recognition (178).…”

Section: Cancer Stem Cells and The Therapeutics That Come From Them: mentioning

confidence: 99%

“…BHF is not a sequence homolog of chordate MHC and has unique sequence features (178). We noted the absence in Botryllus of not only MHC I and II but also immunoglobulin and TCR subgenomic elements (178,185) and the rearrangases Rag1 and 2 (186)-likely brought into vertebrates as elements captured by and transferred horizontally by retroviruses (186)-opening the questions of how and where and from which original DNA sequences these genes of adaptive immunity arose (187).…”

Section: Cancer Stem Cells and The Therapeutics That Come From Them: mentioning

confidence: 99%

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How One Thing Led to Another

Weissman

2016

Annu. Rev. Immunol.

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I started research in high school, experimenting on immunological tolerance to transplantation antigens. This led to studies of the thymus as the site of maturation of T cells, which led to the discovery, isolation, and clinical transplantation of purified hematopoietic stem cells (HSCs). The induction of immune tolerance with HSCs has led to isolation of other tissue-specific stem cells for regenerative medicine. Our studies of circulating competing germline stem cells in colonial protochordates led us to document competing HSCs. In human acute myelogenous leukemia we showed that all preleukemic mutations occur in HSCs, and determined their order; the final mutations occur in a multipotent progenitor derived from the preleukemic HSC clone. With these, we discovered that CD47 is an upregulated gene in all human cancers and is a “don't eat me” signal; blocking it with antibodies leads to cancer cell phagocytosis. CD47 is the first known gene common to all cancers and is a target for cancer immunotherapy.

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Section: Cancer Stem Cells and The Therapeutics That Come From Them: mentioning

confidence: 99%

Section: Cancer Stem Cells and The Therapeutics That Come From Them: mentioning

confidence: 99%

How One Thing Led to Another

Weissman

2016

Annu. Rev. Immunol.

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“…Essentially complete assemblies of the genomes of the probable progenitor species A. duranensis (1.2 Gb) and A. ipanensis (1.5 Gb) were generated and shown to directly align with the genetic map of a cultivated tetraploid peanut 17 . Moleculo synthetic long-read sequencing 18 of the tetraploid peanut genome showed that it was 98-99% identical to the diploid genomes, with differences due to recombination between the subgenomes. A third approach to the deconvolution of polyploid genomes involves the sequencing of DNA from purified chromosome arms.…”

Section: Dna Sequencing and Assembly Technologiesmentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

332

240

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Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...

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“…These patterns raise the intriguing possibility that differential invasive potential has evolved in parallel in each of these lineages. Given that species from two of these species complexes (B. schlosseri and C. intestinalis) are genetic model systems that have had their genomes sequenced (Dehal et al 2002;Voskoboynik et al 2013), it now seems appropriate and possible to leverage high-throughput sequencing technologies to investigate the underpinnings of ascidian invasiveness at the genome level (see recent reviews by Chown et al 2015;Rius et al 2015a). One promising approach would be to use whole-genome re-sequencing or reduced representation libraries to perform population genomic scans for "outlier loci."…”

Section: Interspecific Genetic Diversitymentioning

confidence: 99%