91 Works

Supporting materials from “Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication”

CW Nossa, P Havlak, JX Yue, J Lv, KY Vincent, HJ Brockmann & NH Putnam
Atlantic horseshoe crabs (Limulus polyphemus) are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per...

Genomic data of the Chinese tree shrew (Tupaia chinensis)

Y Fan, Z Huang, C Cao, C Chen, Y Chen, D Fan, J He, H Hou, L Hu, X Hu, X Jiang, R Lai, Y Lang, B Liang, S Liao, D Mu, Y Ma, Y Niu, X Sun, J Xia, J Xiao, Z Xiong, L Xu, L Yang, Y Zhang … & G Zhang
Chinese tree shrews (Tupaia belangeri chinensis) possess many features valuable in animals used as experimental models in biomedical research. Currently, there are numerous attempts to employ tree shrews as models for a variety of human disorders: depression, myopia, hepatitis B and C virus infections, and hepatocellular carcinoma, to name a few. Here we present a publicly available annotated genome sequence for the Chinese tree shrew. Phylogenomic analysis of the tree shrew and other mammalians highly...

Genomic data of the Bald Eagle (Haliaeetus leucocephalus)

W Warren, ED Jarvis, RK Wilson, JT Howard, MTP Gilbert, G Zhang & The Avian Genome Consortium
The Bald Eagle (Haliaeetus leucocephalus(Linnaeus, 1766)) is the official emblem of the United States and it belongs to a group of birds known as fish eagles. They are a large bird with adults weighing upto 4kg.These data have been produced as part of the Avian Phylogenomic Project . DNA was collected from a male bird bred at the NC Raptor Center, Huntersville, North Carolina, USA. The sequencing was conducted at WUSTL. We sequenced the 1.4Gb...

Genomic data of the Great black cormorant (Phalacrocorax carbo)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Great Cormorant (Phalacrocorax carbo) is a widespread member of the cormorant family and is known by several different names around the world - the Black Shag in New Zealand, the Black Cormorant in Australia and the Large Cormorant in India. It is a large black bird that can be distinguished from the Common Shag by its larger size, heavier build and thicker bill. They are mostly silent birds but can produce various guttural noises...

Genomic data of the Great-crested grebe (Podiceps cristatus)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Great Crested Grebe (Podiceps cristatus) is known for its elaborate mating display and is the largest member of the Grebe family in the Old World. In the 19th century, the species was almost hunted to extinction in the UK for its head plumes, which were used to decorate hats and other female attire.These data have been produced as part of the avian phylogenomic project. DNA from the Podiceps cristatus was collected in Denmark. We...

Genomic data of the Bar-tailed trogon (Apaloderma vittatum)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Bar-tailed Trogon (Apaloderma vittatum) belongs to the Trogonidae family of birds and lives in forests at a preferred altitude of around 1600 metres, and who's vocalisations are described "a yelping crescendo". It is found in several African countries - Angola, Burundi, Cameroon, Democratic Republic of the Congo, Equatorial Guinea, and Kenya, to name a few. These data have been produced as part of the avian phylogenomic project. DNA from the Apaloderma vittatum was collected...

Genomic data of the Javan rhinoceros hornbill (Buceros rhinoceros silvestris)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Javan rhinoceros hornbill (Buceros rhinoceros silvestris ) is a sub species of the Rhinoceros Hornbill (Buceros rhinoceros), one of the world's largest hornbills that has lived in captivity for over 90 years. It is found it lowland and tropical and sub-tropical mountain rainforests in Borneo, Sumatra, Java, the Malay Peninsula, Singapore and southern Thailand. It is also the state bird of the Malaysian state, Sarawak. These data have been produced as part of the...

Genomic data of the Red-legged seriema (Cariama cristata)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Red-legged Seriema (Cariama cristata) is a predatory terrestial bird in the Cariamidae family. It is also known as the Crested Cariama. It is found in the grasslands of Brasil, south of the Amazon to Uruguay and northern Argentina. The Red-legged Seriema has a song described to sound like a cross between a bark of a young dog and a clucking of turkeys. These data have been produced as part of the avian phylogenomic project....

Genomic data of the Northern Fulmar (Fulmarus glacialis)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Northern Fulmar (Fulmarus glacialis), also known as Fulmar or Arctic Fulmar, is a highly abundant sea bird and commonly found in north Pacific and north Atlantic subarctic regions. It is a member of the Procellariidae family, which include petrels and shearwaters, and like other petrels, the Northern Fulmar's walking ability is limited but is a very a strong flier. These data have been produced as part of the avian phylogenomic project. DNA from the...

Genomic data of the Chimney swift (Chaetura pelagica)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Chimney Swift (Chaetura pelagica) is a bird belonging to the swift family Apodidae. It is closely related to both the Vaux's Swift and the Chapman's Swift. The Chimney swift is often described as a sociable species, seldom seen alone and only rarely seen at rest. These data have been produced as part of the avian phylogenomic project. DNA from the Chaetura pelagica was collected in USA, Louisiana. We sequenced the genome to a depth...

Genomic data of the Rifleman (Acanthisitta chloris)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Rifleman (Acanthisitta chloris) is an endemic bird to New Zealand and is also known as Tītipounamu in Maori. It belongs to the Acanthisittidae family, also known as New Zealand wrens, and is one of two surviving species. The Rifleman is named after a colonial New Zealand regiment because its plumage is similar to the military uniform of a rifleman.These data have been produced as part of the avian phylogenomic project. DNA from the Acanthisitta...

Annotation and analysis of three crocodilian genomes

RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, MW Vandewege, JA St John, S Capella-Gutiérrez, TA Castoe, C Kern, MK Fujita, JC Opazo, J Jurka, KK Kojima, J Caballero, RM Hubley, AF Smit, RN Platt, CA Lavoie, MP Ramakodi, , A Suh, Isberg, L Miles … & DA Ray
Crocodilians are important model organisms in fields as diverse as developmental biology, osmoregulation, cardiophysiology, paleoclimatology, sex determination, population genetics, paleobiogeography, and functional morphology. Crocodilians, birds, dinosaurs, and pterosaurs comprise a monophyletic group known as the archosaurs. Crocodilians and birds are the only extant members and thus crocodilians (alligators, caimans, crocodiles, and gharials) are the closest living relatives of all birds. To provide context for the diversifications of archosaurs, we generated draft genomes of three crocodilians,...

Supporting material for: \"Rapid detection of structural variation in a Human genome using nanochannel-based genome mapping technology\"

HZ Cao, AR Hastie, D Cao, ET Lam, Y Sun, H Huang, X Liu, L Lin, W Andrews, S Chan, S Huang, X Tong, M Requa, T Anantharaman, A Krogh, H Yang, H Cao & X Xu
The nanochannel-based Genome Mapping technology, commercialized as the Irys Platform, automatically images fluorescently labeled DNA molecules in a massively parallel nanochannel array. This technology has previously been used to map the 4.7-Mb highly variable human MHC region, as well as for de novo assembly of a 2.1-Mb region in the highly complex Aegilops tauschii genome, lending great promise for use in complete genome sequence analysis. Here, we apply this rapid and high-throughput genome mapping method...

Supporting material for \"A data repository and analysis framework for spontaneous neural activity recordings in developing retina\"

SJ Eglen, M Weeks, M Jessop, J Simonotto, T Jackson & E. Sernagor
We present a curated repository of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5. The associated GigaScience paper describes the structure of the data, along with examples of reproducible research using these data files. Citing the data We are grateful to our colleagues for sharing their recordings. If you use any of these data sets, we request that you...

Genomic data of the chickpea (Cicer arietinum)

RK Varshney, C Song, RK Saxena, S Azam, S Yu, AG Sharpe, S Cannon, J Baek, BD Rosen, B Taran, T Millan, X Zhang, LD Ramsay, A Iwata, Y Wang, W Nelson, AD Farmer, PM Gaur, C Soderlund, RV Penmetsa, C Xu, AK Bharti, W He, P Winter, S Zhao … &
Chickpea (Cicer arietinum) is one of the world's most consumed pulses. The Chickpea plant has finely divided leaves, giving it a feathery appearance. The pods are oblong (2 to 3 by 1 to 2 cm) and contain one or two beaked seeds which may be white, yellow, red, brown, or nearly black. They do well in a cool, dry climate and are grown in India as a winter crop. The draft of the chickpea genome...

Genomic data of Flax (Linum usitatissimum)

Z Wang, N Hobson, L Galindo, S Zhu, D Shi, J McDill, L Yang, S Hawkins, G Neutelings, R Datla, G Lambert, DW Galbraith, CJ Grassa, A Geraldes, QC Cronk, C Cullis, PK Dash, PA Kumar, S Cloutier, AG Sharpe, GK Wong, J Wang & MK. Deyholos
Flax (Linum usitatissimum) is also known as linseed. It is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. DNA form the flax was collected in not recorded. We sequenced the unknownGb genome to a depth of approximately 69X with short reads from a series of libraries with various insert sizes ( 300bp, 500bp, 2kb, 5kb and 10kb). The assembled scaffolds of high quality sequences total 25.9G,...

Genomic data of the diploid cotton (Gossypium raimondii)

K Wang, Z Wang, F Li, W Ye, J Wang, G Song, Z Yue, L Cong, H Shang, S Zhu, C Zou, Q Li, Y Yuan, C Lu, H Wei, C Gou, Z Zheng, Y Yin, X Zhang, K Liu, B Wang, C Song, N Shi, RJ Kohel, RG Percy … & S Yu
Cotton is one of the most economically important crop plants worldwide. Its fiber, commonly known as cotton lint, is the principal natural source for the textile industry.We have sequenced and assembled a draft genome of G. raimondii, whose progenitor is the putative contributor of the D subgenome to the economically important fiber-producing cotton species Gossypium hirsutum and Gossypium barbadense. We sequenced the 0.78 Gb genome to a depth of approximately 103 X with short reads...

Genomic data of the pear (Pyrus bretschneideri)

J Wu, Z Wang, Z Shi, S Zhang, R Ming, S Zhu, MA Khan, S Tao, SS Korban, H Wang, NJ Chen, T Nishio, X Xu, L Cong, K Qi, X Huang, Y Wang, X Zhao, J Wu, C Deng, C Gou, W Zhou, H Yin, G Qin, Y Sha … & S Zhang
Pear, the third most important temperate fruit species after grape and apple, belongs to the subfamily Pomoideae in the family Rosaceae. The majority of cultivated pears are functional diploids (2n = 34). The Pyrus genus is genetically diverse with thousands of cultivars, but it can be divided into two major groups, Occidental pears (European pears) and Oriental pears (Asiatic pears). We sequenced the genome to a depth of approximately 107 X with short reads from...

Genomic data of the Killdeer (Charadrius vociferus)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Killdeer (Charadrius vociferus) is a medium-sized plover (a wading bird belonging to the subfamily Charadriinae), and often uses a "broken wing act" to distract predators from their nests. These data have been produced as part of the avian phylogenomic project. DNA from the Charadrius vociferus was collected in Loreto Department, Peru. We sequenced the genome to a depth of approximately 100X with short reads from a series of libraries with various insert sizes (170bp,...

Genomic data of the Golden-collared Manakin (Manacus vitellinus)

G Zhang, B Li, C Li, M.T.P. Gilbert, B Schlinger, E.D. Jarvis, The Avian Genome Consortium & J Wang
The Golden-collared Manakin (Manacus vitellinus (Gould, 1843)) belongs to the Pipridae family of suboscine passseriform birds. It is commonly found in Colombia, Costa Rica and Panama. These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a male obtained in Gamboa, Panama, with the sample obtained by Barney Schlinger of UCLA. We sequenced the genome to a depth of approximately 110X with short reads from a series...

Genomic data of the Hoazin (Opisthocomus hoazin)

G Zhang, B Li, C Li, M.T.P. Gilbert, P. Houde, E.D. Jarvis, The Avian Genome Consortium & J Wang
The Hoazin (Opisthocomus hoazin (Müller, 1776)) is a pheasant-sized tropical bird found in swamps, forest and mangroves of the Amazon and Orinoco Delta in South America. It is known by other names, such as the Hoactzin, Stinkbird or Canje Pheasant and is notable for having chicks that possess claws on two of their wings. These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a female obtained...

Genomic data of the Turkey Vulture (Cathartes aura)

G Zhang, B Li, C Li, M.T.P. Gilbert, J.T. Howard, E.D. Jarvis, The Avian Genome Consortium & J Wang
The Turkey Vulture (Cathartes aura aura (Linnaeus, 1758)), also known as the Turkey Buzzard in North America, is the most widespread vulture species. It lives in a range of open and semi-open areas, such as shrublands, sub-tropical forests and pastures. The Turkey Vulture is a scavanger, feeding exclusively on carrion - it flies low using its keen eye and sense of smell to detect the gases produced during the decay of dead animals. These data...

Genomic data of the Macqueen's Bustard (Chlamydotis macqueenii)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
MacQueen's Bustard (Chlamydotis macqueenii) is a large bird that breeds in southwest Asia in deserts and similarly arid sandy areas. It has recently split as a separate species from the Houbara Bustard of the Canary Islands and Africa, and one difference is that the MacQueen's Bustard has a tendancy to wander compared with the Houbara.These data have been produced as part of the avian phylogenomic project. DNA from the Chlamydotis macqueenii was sequenced to a...

Genomic data of the Speckled mousebird (Colius striatus)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Speckled Mousebird (Colius striatus) is the largest species of mousebird and named because of its overall mousey-brown colour. The bird can be found from Cameroon to Eritrea and Ethiopia, and southern South Africa. Described as a noisy creature, it is not however, known for its voice, and is a rather social bird often observed feeding in groups. These data have been produced as part of the avian phylogenomic project. DNA from the Colius striatus...

Genomic data of the Sunbittern (Eurypyga helias)

G Zhang, B Li, C Li, MTP Gilbert, E Jarvis, The Avian Genome Consortium & J. Wang
The Sunbittern (Eurypyga helias) is the sole member of the family Eurypygidae and is found in Central to South America from Mexico, Peru to Brasil. It has similar morphological features to the Kagu of New Caledonia and is a non-migrant bird that is normally found on the ground scratching for insects. These data have been produced as part of the avian phylogenomic project. DNA from the Eurypyga helias was collected in Denmark. We sequenced the...

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