Genomic Comparison of the Ants
            <i>Camponotus floridanus</i>
            and
            <i>Harpegnathos saltator</i>

Bonasio, Roberto; Zhang, Guojie; Ye, Chaoyang; Mutti, Navdeep S.; Fang, Xiaodong; Qin, Nan; Donahue, Greg; Yang, Pengcheng; Li, Qiye; Li, Cai; Zhang, Pei; Huang, Zhiyong; Berger, Shelley L.; Reinberg, Danny; Wang, Jun; Liebig, Jürgen

doi:10.1126/science.1192428

Cited by 429 publications

(522 citation statements)

References 23 publications

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“…NGS technology has been successfully applied for de novo genome sequencing and assembly using whole-genome shotgun strategies [9][10][11][12][13] . We initially generated 155-fold Illumina whole-genome shotgun reads (Supplementary Table 1), but could not adequately assemble them owing to high levels of polymorphism and abundant repetitive sequences (Supplementary Text B2 and Supplementary Fig.…”

Section: Sequencing and Hierarchical Assemblymentioning

confidence: 99%

The oyster genome reveals stress adaptation and complexity of shell formation

Zhang

Fang

Guo³

et al. 2012

Nature

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The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.Oceans cover approximately 71% of the Earth's surface and harbour most of the phylum diversity of the animal kingdom. Understanding marine biodiversity and its evolution remains a major challenge. The Pacific oyster C. gigas (Thunberg, 1793) is a marine bivalve belonging to the phylum Mollusca, which contains the largest number of described marine animal species 1 . Molluscs have vital roles in the functioning of marine, freshwater and terrestrial ecosystems, and have had major effects on humans, primarily as food sources but also as sources of dyes, decorative pearls and shells, vectors of parasites, and biofouling or destructive agents. Many molluscs are important fishery and aquaculture species, as well as models for studying neurobiology, biomineralization, ocean acidification and adaptation to coastal environments under climate change 2,3 . As the most speciose member of the Lophotrochozoa, phylum Mollusca is central to our understanding of the biology and evolution of this superphylum of protostomes.As sessile marine animals living in estuarine and intertidal regions, oysters must cope with harsh and dynamically changing environments. Abiotic factors such as temperature and salinity fluctuate wildly, and toxic metals and desiccation also pose serious challenges. Filter-feeding oysters face tremendous exposure to microbial pathogens. Oysters do have a notable physical line of defence against predation and desiccation in the formation of thick calcified shells, a key evolutionary innovation making molluscs a successful group. However, acidification of the world's oceans by uptake of anthropogenic carbon dioxide poses a potentially serious threat to this ancient adaptation 4 . Understanding biomineralization and molluscan shell formation is, thus, a major area of interest 5 . Crassostrea gigas is also an interesting model for developmental biology owing to its mosaic development with typical molluscan stages, including trochophore and veliger larvae and metamorphosis.A complete genome sequence of C. gigas would enable a more th...

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Section: Sequencing and Hierarchical Assemblymentioning

confidence: 99%

The oyster genome reveals stress adaptation and complexity of shell formation

Zhang

Fang

Guo³

et al. 2012

Nature

Self Cite

1,925

1,922

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“…The predicted proteomes in the DBM genome and those from the genomes of 11 insect species 13,14,[64][65][66][67][68][69][70][71] and 1 Arachnida outgroup species 72 were used in BLAST (1 × 10 −7 ). The fragmental alignments of HSPs were joined using Solar 36 .…”

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A heterozygous moth genome provides insights into herbivory and detoxification

et al. 2013

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l e t t e r sHow an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants 1 , but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood 2 . We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.The global pest P. xylostella (Lepidoptera: Yponomeutidae) is thought to have coevolved with the crucifer plant family 3 ( Supplementary Fig. 1) and has become the most destructive pest of economically important food crops, including rapeseed, cauliflower and cabbage 4 . Recently, the total cost of damage and management worldwide was estimated at $4-5 billion per annum 5,6 . This insect is the first species to have evolved resistance to dichlorodiphenyltrichloroethane (DDT) in the 1950s 7 and to Bacillus thuringiensis (Bt) toxins in the 1990s 8 and has developed resistance to all classes of insecticide, making it increasingly difficult to control 9,10 . P. xylostella provides an exceptional system for understanding the genetic and molecular bases of how insect herbivores cope with the broad range of plant defenses and chemicals encountered in the environment (Supplementary Fig. 2).We used a P. xylostella strain (Fuzhou-S) collected from a field in Fuzhou in southeastern China (26.08 °N, 119.28 °E) for sequencing ( Supplementary Fig. 1). Whole-genome shotgun-based Illumina sequencing of single individuals (Supplementary Table 1), even after ten generations of laboratory inbreeding, resulted in a poor initial assembly (N50 = 2.4 kb, representing the size above which 50% of the total length of the sequences is included), owing to high levels of heterozygosity ( Supplementary Figs. 3 and 4 and Supplementary Table 2). Subsequently, we sequenced 100,800 fosmid clones (comprising ~10× the genome length) to a depth of 200× ( Supplementary Fig. 5 and Supplementary Tables 3-5), assembling the resulting sequence data into 1,819 scaffolds, with an N50 of 737 kb, spanning ~394 Mb of the genome sequence (version 1; Supplementary Fig. 6 and Supplementary Table 6). The assembly covered 85.5% of a set of protein-coding ESTs (Supplementary Tables 7 and 8) generated by transcriptome sequencing 11 . Alignment of a subject scaffold against a 126-kb BAC (GenBank GU058050) from an altern...

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“…We annotated CSP genes in seven published ant genomes (C. floridanus, Harpegnathos saltator, S. invicta, L. humile, Pogonomyrmex barbatus, Acromyrmex echinatior and Atta cephalotes) (Bonasio et al, 2010;Nygaard et al, 2011;Suen et al, 2011;Wurm et al, 2011) (Figure 1). The abbreviations used here are, respectively, Cflo, Hsal, Sinv, Lhum, Pbar, Aech and Acep.…”

Section: Csp Gene Identificationmentioning

confidence: 99%

Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates

2013

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Gene duplications can have a major role in adaptation, and gene families underlying chemosensation are particularly interesting due to their essential role in chemical recognition of mates, predators and food resources. Social insects add yet another dimension to the study of chemosensory genomics, as the key components of their social life rely on chemical communication. Still, chemosensory gene families are little studied in social insects. Here we annotated chemosensory protein (CSP) genes from seven ant genomes and studied their evolution. The number of functional CSP genes ranges from 11 to 21 depending on species, and the estimated rates of gene birth and death indicate high turnover of genes. Ant CSP genes include seven conservative orthologous groups present in all the ants, and a group of genes that has expanded independently in different ant lineages. Interestingly, the expanded group of genes has a differing mode of evolution from the orthologous groups. The expanded group shows rapid evolution as indicated by a high dN/dS (nonsynonymous to synonymous changes) ratio, several sites under positive selection and many pseudogenes, whereas the genes in the seven orthologous groups evolve slowly under purifying selection and include only one pseudogene. These results show that adaptive changes have played a role in ant CSP evolution. The expanded group of ant-specific genes is phylogenetically close to a conservative orthologous group CSP7, which includes genes known to be involved in ant nestmate recognition, raising an interesting possibility that the expanded CSPs function in ant chemical communication.

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Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator

Cited by 429 publications

References 23 publications

The oyster genome reveals stress adaptation and complexity of shell formation

The oyster genome reveals stress adaptation and complexity of shell formation

A heterozygous moth genome provides insights into herbivory and detoxification

Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates

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