Monthly Archives: September 2012

Comparison with seven other sequenced genomes identified 8,654 oyster-specific genes (Supplementary Text E3.1) that are probably important in the evolution and adaptation of oysters and other molluscs. With oysters being the only representative, these genes could be shared by other molluscs. Among these genes, gene ontology terms related to protein binding, apoptosis, cytokine activity and inflammatory response are highly enriched (P<0.0001; Supplementary Text E2 and Supplementary Table 17), indicating over-representation of some host-defence genes against biotic and abiotic stress. Manual examination shows that several gene families related to defence pathways, including protein folding, oxidation and anti-oxidation, apoptosis and immune responses, are expanded in C. gigas (Fig. 3a and Supplementary Table 18). The oyster genome contains 88 heat shock protein 70 (HSP70) genes, which have crucial roles in protecting cells against heat and other stresses, compared with ~17 in humans and 39 in sea urchins. Phylogenetic analysis finds clustering of 71 oyster HSP70 genes to themselves, suggesting that the expansion is specific to the oyster (Supplementary Fig. 19). Also expanded are cytochrome P450 (Supplementary Fig. 20) and multi-copper oxidase gene families, which are important in the biotransformation of endobiotic and xenobiotic chemicals26, and extracellular superoxide dismutases, which are important in defence against oxidative stress. The oyster genome has 48 genes coding for inhibitor of apoptosis proteins (IAPs), compared with 8 in humans and 7 in sea urchins, indicating a powerful anti-apoptosis system in oysters. Genes encoding lectin-like proteins, including C-type lectin, fibrinogen-related proteins and C1q domain-containing proteins (C1QDCs), are highly over-represented in the oyster genome (P<0.0001; Supplementary Table 18); these genes have important roles in the innate immune response in invertebrates27, 28, 29. Interestingly, many immune-related genes, including genes coding for Gram-negative bacteria-binding proteins, peptidoglycan-recognition proteins, defensin, C-type-lectin-domain-containing proteins and C1QDCs, are highly expressed in the digestive gland (Supplementary Fig. 21), indicating that the digestive system of this filter feeder is an important first-line defence organ against pathogens.

a, Expansion and expression of key genes in major stress-response pathways in C. gigas. Genes include HSPs and HSF in the heat-shock response; GRP78, CRT, CNX, GRP94, PERK, IRE1 and EIF2a in the endoplasmic reticulum unfolded-protein response (UPRER); IAPs, BCL2 like, BAG, BI1, caspases, FADD and TNFR in apoptotic pathways; CYP450 and MO in oxidation; and SOD, GPX, PRX and CAT in anti-oxidation. Boxes with bold black borders indicate gene families (HSPs, IAPs and SODs) expanded in C. gigas, and the filled colours correspond to their degree of upregulation in RPKMtreatment/RPKMcontrol by stress, found in 61 transcriptomes from oysters challenged with 9 types of stressors (Supplementary Text G2 and Supplementary Table 23). b, Venn diagram of common and unique genes expressed in response to temperature, salinity, air exposure and heavy-metal stress (zinc, cadmium, copper, lead and mercury), showing overlap of responses. c, Number of genes with and without detectable paralogues differentially expressed under stress and normal conditions, showing that genes responding to stress are more likely to have paralogues (P<11010; 2 test). Green sections of the pie chart represent 1,442, 809, 358, 550 and 7,938 paralogues for air exposure, metal, temperature, salinity and normal conditions, respectively.

To investigate genome-wide responses to stress, we sequenced 61 transcriptomes from C. gigas subjected to nine stressors, including temperature, salinity, air exposure and heavy metals (Supplementary Text G1 and Supplementary Tables 19 and 20). We found that 5,844 genes were differentially expressed under at least one stressor, and genes responding to different stressors showed significant overlap (Fig. 3b and Supplementary Fig. 23a). Air exposure induced a response from the largest number of genes (4,420), indicating that air exposure is a major stressor and that oysters have evolved an extensive gene set in defence. Genes differentially expressed in response to stress are more likely to have paralogues (Fig. 3c), suggesting that expansion and selective retention of duplicated defence-related genes are probably important to oyster adaptation. Under most stressors, genes coding for HSPs, histones, IAPs and protein biogenesis were upregulated, and those for protein degradation downregulated, pointing to concerted responses to maintain cellular homeostasis30 (Supplementary Text G3 and Supplementary Table 21). Genes involved in the unfolded protein response to cellular stress in the endoplasmic reticulum (coding for calreticulin, calnexin, 78- and 94-kDa glucose-regulated proteins) were upregulated, indicating that protein quality control is critical in cellular homeostasis under stress.

Air exposure induced up to 67-fold upregulation of five highly expressed IAPs (Supplementary Fig. 24a). Other inhibitors of apoptosis were also upregulated: BCL2 up to fourfold and BAG up to 12-fold (Supplementary Fig. 24b). These apoptosis inhibitors were also highly upregulated under heat and low salinity stress. These findings, along with the expansion of IAPs, suggest that a powerful anti-apoptosis system exists and may be critical for the amazing endurance of oysters to air exposure and other stresses. The existence of an intrinsic apoptosis pathway in invertebrates has been controversial, and parts of the pathways have only recently been demonstrated for two lophotrochozoans31, 32. The finding of key genes belonging to both intrinsic (BAX, BAK, BAG, BCL2, BI1 and procaspase) and extrinsic (TNFR and caspase 8) apoptosis pathways indicates that oysters have advanced apoptosis systems. Powerful inhibition of apoptosis as shown by genomic and transcriptomic analyses may be central to the ability of oysters to tolerate prolonged air exposure and other stresses.

Heat stress induced a ~2,000-fold increase in expression of five highly inducible HSP70 genes or a 13.9-fold increase in average expression of all HSP70 genes, amounting to 4.2% of all transcripts (Supplementary Figs 24c and 25). The genomic expansion and massive upregulation of HSP genes help to explain why C. gigas can tolerate temperatures as high as 49C when exposed to summer sun at low tide33. HSP genes were also upregulated under other stressors and may be central to the oyster defence against all stresses (Supplementary Fig. 25). HSP genes may also inhibit apoptosis by binding to effector caspases34.

Genes involved in signal transduction, including genes coding for G-protein-coupled receptors and Ras GTPase, were also activated by stressors (Supplementary Fig. 24f) and over-represented in the oyster genome (Supplementary Table 11). These regulators may have a role in orchestrating stress responses, which seem to be well coordinated (Fig. 3a and Supplementary Fig. 25). The expansion of key defence genes and the strong, complex transcriptomic response to stress highlight the sophisticated genomic adaptations of the oyster to sessile life in a highly stressful environment.

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The oyster genome reveals stress adaptation and complexity of shell formation

Public release date: 19-Sep-2012 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

September 19, Shenzhen, China An international research team, led by Institute of Oceanology of Chinese Academy of Sciences and BGI, has completed the sequencing, assembly and analysis of Pacific oyster (Crassostrea gigas) genomethe first mollusk genome to be sequencedthat will help to fill a void in our understanding of the species-rich but poorly explored mollusc family. The study, published online today in Nature, reveals the unique adaptations of oysters to highly stressful environment and the complexity mechanism of shell formation.

"The accomplishment is a major breakthrough in the international Conchological research, with great advancement in the fields of Conchology and Marine Biology." said, Professor Fusui Zhang, Academician of Chinese Academy of Sciences, and a well-known Chinese Scientist of Conchology, "The study will provide valuable resources for studying the biology and genetic improvement of molluscs and other marine species. "

Oysters are a soft-bodied invertebrate with a double-hinged shell, which make up an essential part of many aquatic ecosystems. They have a global distribution and for many years they have much higher annual production than any other freshwater or marine organisms. In addition to its economic and ecological importance, the unique biological characteristics of oyster make it an important model for studying marine adaptations, inducing a great deal of biological and genomics research. The completed sequencing of oyster genome will provide a new horizon into understanding its natural mechanisms such as the adaptations to environmental stresses and shell formation, better exploration of marine gene resource, , among others.

Unlike many mammals and social insects, oyster as well as many other marine invertebrates is known to be highly polymorphism, which is a challenge for de novo assembling based on current strategies. In this study, researchers sequenced and assembled the Pacific oyster genome using a combination of short reads and a "Divide and Conquer" fosmid-pooling strategy. This is a novel approach developed by BGI, which can be used to study the genomes with high level of heterozygosity and/or repetitive sequences. After data process, the assembled oyster genome size is about 559 Mb, with a total of ~28,000 genes.

Based on the genomic and transcriptomic analysis results, researchers uncovered an extensive set of genes that allow oysters to adapt and cope with environmental stresses, such as temperature variation and changes in salinity, air exposure and heavy metals. For example, the expansion of heat shock protein 70 (HSP 70) may help explain why Pacific oyster can tolerate high temperatures as HSP family is expanded and highly expressed when in high temperature. The expansion of inhibitors of apoptosis proteins (IAPs), along with other findings, suggested that a powerful anti-apoptosis system exists and may be critical for oyster's amazing endurance to air exposure and other stresses. One notable finding on development is that the oyster Hox gene cluster was broken, and there are unusual gene losses and expansions of the TALE and PRD classes. Hox genes are essential and play critical important role in body plan, the Hox clusters are found to be more conserved in many organisms.

Researchers found paralogs might have the function to change the gene expression for better coping with the stresses. This result suggested that expansion and selective retention of duplicated defense-related genes are probably important to oyster's adaptation. Moreover, many immune-related genes were highly expressed in the digestive gland of the oyster, which indicated its digestive system was an important first-line defense organ against pathogens for the filter-feeder. The shell provides a strong protection against predation and desiccation in sessile marine animals such as oysters. At present, two models have been proposed for molluscan shell formation, but neither of them is accurate enough. In this study, by sequencing the peptides in the shell, researchers identified 259 shell proteins, and further analysis revealed that shell formation was a far more complex process than previously thought. They found many diverse proteins may play important roles in matrix construction and modification. The typical ECM proteins such as Laminin and some collagens were highly expressed in shells, suggesting that shell matrix has similarities to the ECM of animal connective tissues and basal lamina. Hemocytes may mediate fibronectin (FN)-like fibril formation in the shell matrix as they do in ECM. Furthermore, the functional diversity of proteins showed that the cells and exosome may participate in the shell formation.

Xiaodong Fang, Primary Investigator of this project at BGI, said, "The assembly approach of Oyster genome opens a new way for researchers to better crack the genomes with high-heterozygosity and high-polymorphism. The Oyster genome sheds insights into the comprehensive understanding of mollusc genomes or even lophotrochozoa genomes at the whole genome-wide level, with focuses on the studies of diversity, evolutionary adaptive mechanisms, developmental biology as well as genomics-assisted breeding. "

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Oyster genome uncover the stress adaptation and complexity of shell formation

A Bangladeshi scientist has decoded the genome of a most deadly fungus that causes havoc to global jute and soybean production.

The fungus -- macrophomina phaseolina -- also causes seedling blight, root rot and charcoal rot of more than 500 crop and non-crop species.

The gene sequencing of macrophomina phaseolina would particularly help Bangladeshi scientists to develop jute varieties capable of fighting the fungus that causes an annual yield loss of around 40 billion taka (US$489.45 million) damaging 30 per cent of the country's precious natural fibre, experts said.

Jute is the second largest fibre crop next to cotton. And Bangladesh is the world's second-biggest producer of jute, next to India, and the biggest exporter of the natural fibre.

Bangladesh's globally famed geneticist Dr Maqsudul Alam led a 17-member team since early last year to decode the deadly fungus. The decoding has been done at a recently set up laboratory at Bangladesh Jute Research Institute (BJRI).

Prime Minister Sheikh Hasina announced the scientific achievement of Bangladesh in the Jatiya Sangsad yesterday amid cheers and desk thumping by lawmakers.

Dr Alam and his team's success in decoding fungus genome came just two years after he had decoded jute genome. Maqsudul Alam earlier sequenced the genome of papaya in the United States and rubber plant in Malaysia.

"Macrophomina phaseolina damages jute stems and is responsible for 30 per cent of jute yield loss. Besides, it also causes multiple damage to 500 crop and non-crop species. The US alone suffers 15 billion taka production loss a year due to "charcoal rot" in soybean caused by macrophomina phaseolina," explained biotechnologist Dr Shahidul Islam, a senior member of Dr Alam's team.

Reached over the phone last night, Dr Islam said they had completed the sequencing earlier this year but it has been internationally recognised with its publication in acclaimed UK journal BMC Genomics on September 17.

Genome sequencing helps scientists find genes much more easily and quickly. It allows scientists identify and understand how genes work together on a plant's various features like growth, development and maintenance as an entire organism. This allows them to manipulate the genes and enhance, reduce or add certain features of the plant.

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Bangladeshi scientist decodes genome of deadly fungus

Image of fresh Pacific oyster courtesy of Guofan Zhang, photo by Tao Liu

The world of the mollusk genome is now our oyster, as researchers have now sequenced the genetic code of this hearty (and delicious) shellfish, revealing it to be even more complex and adaptable than previously imagined.

The new genome provides insights how oysters manage to cope with a dynamic habitat and how they build their shells. The genome of the Pacific oyster (Crassostrea gigas) contains approximately 28,000 genes (compared with the 20,000 or so genes of humans), some 8,654 of which are thought to be specific to oystersor at least to mollusks.

One of the big mysteries surrounding oysters and many other mollusks is how they manage to thrive in such variable marine environments. As sessile creatures that largely stay put, they endure extreme temperature changes, swings in salinity, and prolonged exposure to open air in the intertidal zone. The researchers found 88 different genes that code for so-called heat shock protein 70, which guards cells and tissue against hot temperatures. This extra buffering might explain why oysters can survive in the sun in temperatures up to about 49 degrees Celsius (120 degrees Fahrenheit). By contrast, humans have about 17 genes that make this protein, and even relatively immobile sea urchins have just 39.

Oysters are known for being excellent water filterers, and some environmental groups have even proposed reintroducing these shellfish to New York City waterways to clean up the harbor. How can these oysters stay healthy with so many chemicals and heavy metals flowing through them? The genome reveals one of the oysters secrets: a highly active immune systemespecially in its gut. The researchers found that many of the genes that make immune-related proteins are expressed in the oysters so-called digestive gland, indicating that the digestive system of this filter feeder is an important first-line defense organ against pathogens, the authors noted in their paper published online September 19 in Nature (Scientific American is part of Nature Publishing Group).

Perhaps the key to the survival of this soft-bodied organism is its flexible genome. The researchers sequenced 61 transcriptomes (RNA in the cell or tissue) and then exposed them to familiar oyster stressors. When exposed to air, for example, 4,420 different genes altered their expression. And some exposures produced impressive results. Exposing the transcriptomes to heat invoked a roughly 2,000 times higher expression of five of the heat shock protein 70-coding genes.

The genome of the oyster, the first mollusk to be sequenced, also cracked open some evolutionary clues about the shell of these tenacious bivalves. Once thought to be a fairly simple, self-assembling matrix of calcium carbonate, it now looks to be a complex creation that has undergone eons of evolutionary tweaking. And it shares some surprising signatures with the cell walls of other animals, suggesting that shell formation is an active and elaborate process that involves hundreds of proteins.

The oyster genome had thwarted standard sequencing techniques because it repeats itself in many placesand in others has different codes in the same places in a single individual. So the researchers tried a fosmid-pooling strategy, which allowed them to divide the genome up and compare multiple sequencings of each area. To help the process along further, they also created a more genetically homogenous oyster, using one from four generations of direct sibling inbreeding. They then compared this to a wild-caught oyster, just to make sure their results were not too altered by the chosen individual.

The success with the oyster genome will help open the door to sequencing more of the highly diverse mollusks, including snails, scallops and, perhaps even the master RNA editors themselves, the octopuses. Information from the oyster genome and other sequences in this group could help researchers better understand these organisms role in the oceans, their evolution and how they respond to climate change and ocean acidification as well as better strategies for raising them.

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Oyster Genome Pries Open Mollusk Evolutionary Shell