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Database of colors mapped to species

Database of colors mapped to species


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I was wondering about the physics of color, and now am interested in finding out if there are any resources (databases, text files, html tables, or pdf listings) of species and their associated colors or (ideally) color wavelength spectrum.

For example, a rose bush might have a pink (flower) color spectrum and a green (leaf) and brown (stem) color spectrum. A worm might have a brown and pink color spectrum. A lion might have a yellow and brown and gold color spectrum. Wondering (a) if any of this information is captured in any form on the web (such as 1 journal article per species), and (b) if it is aggregated into a database, text file, table, or other sort of list which includes lots of species (animals, plants, fungi, rocks, etc.), so it would say the wavelength of visible light that it emits, or some ranges of it, or even a hex color range.


Database of colors mapped to species - Biology

Mammal Species of the World, 3rd edition (MSW3) is a database of mammalian taxonomy. It is hoped that this database on the World Wide Web can be used as a convenient on-line reference for identifying or verifying recognized scientific names and for taxonomic research. The names are organized in a hierarchy that includes Order, Suborder, Family, Subfamily, Genus, Species and Subspecies. Records include the following fields:

  • Scientific name
  • Author's name and year described
  • Original publication citation
  • Common name
  • Type Species
  • Type Locality
  • Distribution
  • Comments
  • Status
  • Synonyms

The citation for this work is: Don E. Wilson & DeeAnn M. Reeder (editors). 2005. Mammal Species of the World. A Taxonomic and Geographic Reference (3rd ed), Johns Hopkins University Press, 2,142 pp. (Available from Johns Hopkins University Press, 1-800-537-5487 or (410) 516-6900, or at http://www.press.jhu.edu).

This third edition is enhanced by the identification of subspecies, and by the inclusion of authority information for all synonyms. Further information about the book and about the contents of each field can be found in the preface and introductory material.

This online list was compiled under the auspices of the American Society of Mammalogists. Copyright 2005 Johns Hopkins University Press. All rights are reserved. The data in this checklist of mammal species of the world are being presented for non-commercial, personal, and collections management use only. Copying or redistributing these data in any manner for personal or corporate gain is not permitted. A list of the authors responsible for various portions of the text can be found here.

For an analysis of new species found in the third edition see: D. M. Reeder , K. M. Helgen, and D. E. Wilson. 2007. Global Trends and Biases in New Mammal Species Discoveries. Occasional Papers, Museum of Texas Tech University, 269:1-36. pdf [ click here].

This project is in collaboration with the Division of Mammals of the Department of Vertebrate Zoology at the National Museum of Natural History, Smithsonian Institution and The American Society of Mammalogists.

The scientific names from the MSW3 database are available as a custom dictionary that can be used with various Microsoft Office applications. To download the dictionary, right-click on this link and choose 'Save Target As . ' (or the equivalent, depending on the browser that you are using). [Installation instructions for custom dictionaries vary depending on the version of Microsoft Office that you are using. To start, try here.] Thanks to Doug Kelt, UC Davis, for creating and sharing this dictionary.


Galeocerdo cuvier

Tiger shark in the Bahamas. Photo © David Snyder

Tiger sharks are named for their distinctive color pattern. The body is gray with dark gray vertical bars or spots on the flanks with a pale or white underside. The markings are especially distinctive in juveniles but diminish with age. Tiger sharks are among the largest of the sharks and are recorded up to 550 cm (18 ft) long. They are known to eat most marine animals, sea birds, the occasional terrestrial animal and even garbage encountered floating at sea. Despite being a large slow-moving shark, it is a highly effective ambush predator that deploys short bursts of speed to secure its prey (Simpfendorfer 2009).

Fun Fact: Tiger sharks, bull sharks, and white sharks are commonly referred to as “The Big Three” for their involvement in shark attacks. These species are readily identified by the victims and witnesses. In cases involving smaller requiem sharks, the species involved are seldom identified as they are harder to tell apart.

Order – Carcharhiniformes Family – Carcharhinidae Genus – Galeocerdo Species – cuvier

Common Names

Africaans: Tierhaai
Arabic: Jarjur, Jarjur knaza
Creole: Requin tigre
Dutch: Tijgerhaai
English: Tiger shark, leopard shark, maneater shark, and spotted shark
Fijian: Qio saga
Finnish: Tiikerihai
French: Mangeur d’hommes, Requin demoiselle, Requin tigre commun, Requin-tigre
German: Tigerhai
Gujarati: Bhoavar
Greek: Carcharias
Hawaiian: Mano pa’ele
Icelandic: Tígrisháfur
Italian: Squalo tigre
Japanese: Itachizame
Kannada: Pilithatte
Kiribati: Te babatababa
Malay: Cucut macan
Malayalam: Pulli sravu
Maori: Mgutukao
Polish: Zarlacz tygrysi
Portuguese: Cação cabeça-chata, Jaguara, Marracho tigre, Tigre, Tintureira
Rapa: Ma`o patapata
Samoan: Naiufi
Spanish: Alecrin, Amarillo, Cabron, Tiburón tigre, Tintorera
Swahili: Amzani
Tagalog: Pating
Tamil: Wulluven sorrah
Tahitian: Ma’o tore tore
Telugu: Kethulam

Importance to Humans

Tiger shark caught during a fishing derby off Jacksonville, Florida in 1981. Photo © FLMNH

Tiger sharks are targeted directly for their fins, flesh, and oil and indirectly as bycatch in commercial and recreational fisheries worldwide. Shark fishery catches of tiger sharks are documented from the western Atlantic, Australia, India, Papua New Guinea, Brazil, and Taiwan. In the United States, tiger sharks are the third most common of the large, coastal sharks caught. Historically, tiger shark liver was used to produce oil rich in vitamin A while its thick, tough skin was used for quality leather. Tiger shark leather has long been used to make traditional Hawaiian drums. Besides its significance to the fishing industry, the tiger shark remains a highly sought-after big game fish in worldwide recreational fisheries (Simpfendorfer 2009).

Danger to Humans

The tiger shark is a formidable predator and second only to the white shark (Carcharodon carcharias) in terms of the number of reported attacks on humans. Tiger sharks are often curious and unaggressive when encountered (Compagno et al. 2005) yet are one of the three species most commonly implicated in shark attacks and fatalities and show should be treated with extreme caution and a great deal of respect (ISAF 2018).

Conservation

IUCN Red List Status: Near Threatened

Both commercial and recreational fishing catch rates for this species in the mid-Atlantic region have declined since the mid-1980’s. Data taken by observers on commercial fishing boats indicate that fishing pressure, particularly on juveniles has adversely affected the size of the population. The World Conservation Union (IUCN) lists the tiger shark as “Near Threatened” throughout its range. However, they do not face a high risk of extinction at the present time.

The IUCN is a global union of states, governmental agencies, and non-governmental organizations in a partnership that assesses the conservation status of species.

Geographical Distribution

World distribution of the tiger shark. Map © Chondrichthyan Tree of Life

The tiger shark is found throughout the world’s temperate and tropical waters, with the exception of the Mediterranean Sea. It is a wide-ranging species that is at home both in the open ocean as well as shallow coastal waters. Reports of individuals from as far north as Iceland and the United Kingdom have been confirmed, but these instances are likely the result of roaming sharks following the warmer Gulf Stream north across the Atlantic (Simpfendorfer 2009).

Habitat

This shark has a notable tolerance for many different kinds of marine habitats but generally prefers murky waters in coastal areas. It is commonly found in river estuaries, harbors, and other inlets where runoff from the land provides suitable habitat for a variety of prey items. Tiger sharks also occur in shallow areas around large island chains, including the lagoons and coral atolls found on the coasts of oceanic islands (Compagno et al. 2005). It is often seen at the surface but has been reported at depths of 350 m (1085 ft) (Simpfendorfer 2009).

Tiger sharks undergo seasonal migrations. They move into temperate waters from the tropics in warmer months and return to the tropics during the winter. They also make long oceanic migrations between islands and are capable of traveling long distances in a short amount of time (Simpfendorfer 2009).

Distinguishing Characteristics

Tiger shark (Galeocerdo cuvier). Illustration courtesy FAO, Species Identification and Biodata

1. Dorsal surface of juveniles have blotched coloration that fuse together to form tiger-like stripes as the shark grows. (This coloration fades and the stripes become less distinct in mature adults)

2. Snout is blunt and wide

Tiger Shark. Photo © John Soward

Biology

Probably the most easy to recognize of the requiem sharks, the tiger gets its name from dark spots and vertical bars that run the length of the body. The anterior portion of the body is stout but becomes increasingly slender posterior to the abdomen. The tiger shark has a robust head with large eyes and a conspicuously blunt snout. The mouth is large with long labial furrows at the corners of the jaw. The broad first dorsal fin originates posterior to the pectoral axil. The much smaller second dorsal fin initiates anterior to the origin of the strongly recurved anal fin. A ridge is present along the back between the two dorsal fins. A low longitudinal keel is present on the caudal peduncle and the upper lobe of the caudal fin is long and thin with a subterminal notch (Compagno et al. 2005).

Juvenile Tiger shark showing color pattern. Photo © George Burgess

Coloration
Dark gray or black dorsal surface with a pale stark white underbelly. The characteristic dark spots and stripes are most prominent in young sharks and fade as the shark matures.

A) Upper and lower teeth of Galeocerdo cuvier, and B) Juvenile tiger shark showing dentition. Illustration courtesy Casey (1964) Bur. Sport Fish. & Wildl Circ. 179 and photo © George Burgess

Dentition
The tiger shark has very distinct dentition. The jaws house large teeth with curved cusps and finely serrated edges. Each tooth has a deep notch on the outer margin lined with numerous cusplets. Teeth are similarly shaped in both upper and lower jaws decreasing in size toward the back of the jaw, toward the corner of the mouth as is the case for most sharks.

Size, Age, and Growth
One of the largest sharks, the tiger shark commonly reaches a length of 325-425 cm (10-14 ft) and weighs over 385-635 kg (850-1400 lbs). Length at birth varies from 51-76 cm (1-1.5 ft). Males reach sexual maturity at 226-290 cm (7-9 ft), while females become mature at 250-325 cm (8-10 ft) (Compagno et al. 2005). The largest specimens attain lengths of over 5.5 m (18 ft) and are estimated to weigh over 900 kg (2000 lbs).

Tiger sharks feed on the green sea turtle. Photo courtesy NOAA

Food Habits
Undoubtedly the least discriminative all species, the tiger shark has a reputation as an animal that will eat almost anything (Compagno et al. 2005). Preferred prey varies depending upon geographical region but commonly includes sea turtles, rays, other sharks, bony fishes, sea birds, dolphins, squid, various crustaceans and carrion. The tiger shark’s highly serrated teeth combined with the saw-like action from shaking the head back and forth allows it to tear chunks from much larger marine animals. Interestingly, it is not uncommon to find objects of human origin in this animal’s stomach. One large female caught off the north end of the Gulf of Aqaba in the Red Sea contained two empty cans, a plastic bottle, two burlap sacks, a squid, and a 20 cm (8 in) fish. Garbage and refuse is often recovered from the stomachs of sharks caught in harbors and river inlets, where it is commonly dumped into the water. Although far from a natural food item, human remains sometime end up in the guts of these scavenging sharks. Tiger sharks are solitary hunters that feed primarily at night as the shark moves further inshore and closer to the surface. They are sometimes seen in groups, but this is probably driven by food availability rather than social behavior.

Female tiger shark with mating scars from bites of male during mating attempts. Photo © Doug Perrine

Reproduction
The tiger shark employs a highly unusual reproductive strategy. It gives birth to live young as do its close relatives the hammerheads and the requiem sharks, but unlike these species it, does not use a placenta to nourish the developing embryos. Instead tiger shark embryos develop from relatively large eggs in the initial stages of development. When the yolk supply is used up the developing embryo switches over to drinking uterine fluid as a source of nutrition, through a process termed “embryotrophy”, during the later stages of development. (Castro et al. 2015) This mode of reproduction, in which animals are born alive but are not nourished through a placenta is broadly referred to as ovoviviparity. The gestation period ranges from 13-16 months, at which time a female can give birth to anywhere from 10 to 82 pups. In the Northern Hemisphere, mating takes place between March and May and the young are born between April and June of the following year. In the Southern Hemisphere, it is believed that pupping occurs in November to January (Simfendorfer 2009).

Taxonomy

First described by Peron and Lessueur in Lessueur (1822), the tiger shark was given the name Squalus cuvier. Later, Muller and Henle (1837) designated Squalus arcticus (Faber, 1829) as the type species and suggested the name Galeocerdo tigrinus. Various synonyms have been used since including: Galeus cepedianus Agassiz 1838, Galeus maculatus Ranzani 1840, Carcharias fasciatus Bleeker 1852, Galeocerdo rayneri McDonald & Barron 1868, Galeocerdo obtusus Klunzinger 1871, and Carcharias hemprichii Klunzinger 1871. The genus name Galeocerdo is derived from the ancient Greek, “γαλεος” (galeos) = Aristotle’s shark and “κερδω” (kerdo) = the fox.

References

Castro, J.I., Sato, K., & Bodine, A.B. (2016) A novel mode of embryonic nutrition in the tiger shark, Galeocerdo cuvier, Marine Biology Research, 12:2, 200-205, DOI: 10.1080/17451000.2015.1099677

Compagno, L., Dando, M., & Fowler, S. (2005) A Field Guide to the Sharks of the World. London: Harper Collins Publishers Ltd.


Abstract

Planeación de la Conservación en las Fronteras de China con Myanmar, Laos y Vietnam

Resumen

La conservación transfronteriza cada vez juega un papel más importante en la preservación de la integridad del ecosistema y en el freno a la pérdida local de la biodiversidad causada por las actividades antropogénicas. Sin embargo, la falta de información sobre la distribución de las especies en las regiones transfronterizas y de la comprensión de las amenazas en estas áreas obstaculiza la conservación. Desarrollamos un plan de conservación espacial para las áreas transfronterizas entre la provincia de Yunnan, al suroeste de China, y los países vecinos Myanmar, Laos y Vietnam localizadas en el punto caliente de biodiversidad Indo-Burma. Para identificar las áreas prioritarias para la conservación y la restauración, determinamos los patrones de distribución de las especies y los recientes cambios en el uso de suelo y examinamos las dinámicas espaciotemporales del bosque natural conectado, el cual mantiene a la mayoría de las especies. Evaluamos la conectividad con el área equivalente conectada (AEC), que es la cantidad de hábitat accesible para una especie. Un AEC incorpora la presencia del hábitat en un fragmento y la cantidad de hábitat en otros fragmentos dentro de la distancia de dispersión. Analizamos 197,845 registros de localidades desde colecciones de especímenes y monografías para 21,004 especies de plantas y de vertebrados. La región de Yunnan inmediatamente adyacente a las fronteras internacionales tuvo la riqueza de especies más alta con el 61% de las especies registradas y el 56% de los vertebrados amenazados, lo que sugiere un elevado valor de conservación. Las imágenes satelitales mostraron que el área del bosque natural en la zona fronteriza declinó en un 5.2% (13,255 km 2 ) entre 1995 y 2018 y que los sembradíos de monocultivos incrementaron en un 92.4%, los matorrales en un 10.1% y otras tierras de cultivo en un 6.2%. La declinación resultante en el bosque natural conectado redujo la cantidad del hábitat, especialmente para los especialistas del bosque con habilidades limitadas de dispersión. La declinación más grave en la conectividad ocurrió a lo largo de la frontera entre China y Vietnam. Muchas áreas prioritarias atraviesan las fronteras internacionales, lo que indica una demanda y un potencial para el establecimiento de áreas protegidas transfronterizas. Nuestros resultados ejemplifican la importancia de la cooperación bi- y multilateral para proteger la biodiversidad en esta región y proporciona información para la planeación y práctica de la conservación en el futuro.


Interesting Insights from the Fallow Deer!

The fallow deer has been part of human history likely since humans were “human.” Not surprisingly, the fallow deer has many lessons about important biological concepts! The following are some of the most important things this species can teach us about biology:

“The Rut” – A Timing Strategy

Female estrous cycles generally drive the rut, since the females only come into estrous once per year. Thus, males only have a limited opportunity to reproduce and must try to impregnate as many females as possible. During the rut, fallow deer bucks can have different strategies for attracting mates, depending on the environment and local population size.

Species Transplanted by Humans

If you look at the map of fallow deer populations below, it might be surprising to see that the fallow deer has several distinct populations that are spread throughout the globe. In fact, the different colors on this map correspond to different expansions of the fallow deer range over time.

The historical population in brown (1) represents the oldest known population of fallow deer. These populations have been hunted by humans for hundreds of thousands of years. The red population (2), likely represents an expansion of the original population brought to Greece by ancient civilizations.

The purple population (3) represents the Roman expansion of the fallow deer population, with historical records showing that the deer were brought along with Roman armies and were encouraged to form wild populations. These efforts likely carried fallow deer into many parts of Europe.

The last population, in teal (4), represents the “modern” introductions of fallow deer that have happened since the early 1900s. The fallow deer has found its way to North America, South America, South Africa, Australia, and New Zealand – most from the import of live animals for hunting.

In places like Texas and Argentina, fallow deer are often farmed on ranches. “Hunts” for these deer are sold to wealthy gun-owners, though subsistence hunting of fallow deer has not occurred in a long time. Ecologists must watch these introduced populations carefully, to ensure they do not cause damage like the cane toad, zebrafish, or other invasive species.

Polygyny in Different Ecosystems

Like many other cervids, fallow deer practice polygyny. “Poly-” means many, whereas “gyne” means “wive” – together, “many wives.”

Animals that practice polygyny form groups with one male for many females. It is opposed to polyandry, where one female controls a group of many males (sometimes seen in fish). A polygynous species can operate under different rules, depending on the environment, species density, and local behaviors.

Fallow deer have been observed practicing two kinds of polygyny: Harems and Lekking. Males that form harems stay with the group as it moves about. The male will typically try to keep his females herded together, so no other males can sneak in to get access. By contrast, lekking males defend a valuable territory – or lek – that females wander into. While they are in his territory, only he can try to copulate.

Studies have shown that which method a population of fallow deer chooses depends largely on the local environment. When females move long distances in resource-scarce areas, males tend to form harems to protect them. When females are located in an area with many resources, males will tend to protect the best areas where the most females hang out. This is not an easy feat for males either way – researchers have shown that male fallow deer can lose up to 17% of their body weight during the rut, as they try to defend females or territory.


Background

Systems biology is a research field that analyzes large amounts of omics data bioinformatically, constructs models for biological systems, and confirms model-driven hypotheses using biological experiments (Kitano 2002 Sauer et al. 2007). This approach provides a general biological view that is difficult to build using a single approach (Fang and Casadevall 2011). It is also a field of multi-disciplinary research that cannot be distinguished from the definition of bioinformation (Vincent and Charette 2015).

Systems biology expedites understanding of human cancer, diabetes, and Parkinson’s disease (Du and Elemento 2015 Bakar et al. 2015 Michel et al. 2016), reconstructs the metabolism pathways of microbes and algae to make cell factories (De Bhowmick et al. 2015 Nielsen and Keasling 2016), and explores synthetic biology (Andrianantoandro et al. 2006 Barrett et al. 2006 Cameron et al. 2014). In plant research, high-throughput technologies have been introduced (Yin and Struik, 2010 Glinski and Weckwerth 2006 Egan et al. 2012) and facilitate a large amount of research (Yuan et al. 2008 Fernie 2012). For example, plant systems biology has produced new understandings of metabolism (Schauer and Fernie 2006 Last et al. 2007 Sweetlove et al. 2014), stress responses (Cramer et al. 2011 Jung et al. 2013 Nakabayashi and Saito 2015), and integrative omics research (Rajasundaram and Selbig 2016). Also, together with CRISPR/Cas9 genome editing technology, plant synthetic biology has been established (Liu and Stewart Jr 2015 Baltes and Voytas 2015).

The world demand for staple crops is expected to increase by 60% from 2010 to 2050 (Fischer et al. 2014). Rice, wheat, and maize are the big three global cereals that together account for

87% of all grain production worldwide. Rice is a model crop plant it was the first plant whose whole genome information was sequenced among cereal crops (Goff et al. 2002 International Rice Genome Sequencing Project 2005), and extensive genetic studies and technological platforms have been established for functional genomic research in rice. Major goals of rice research are to identify the functional diversity of every gene and improve the crop’s agronomic traits (Zhang 2007 Zhang et al. 2008). To that end, multi-omics data have been developed using new technologies, including next generation sequencing (NGS), and many gene-indexed mutants mediated by T-DNA or transposable element insertion have been constructed (Wei et al. 2013). These resources facilitate functional genomics as of 2017, around 3000 genes in rice had been functionally identified (Jiang et al. 2012 Yao et al. 2018). Along with ever-increasing information about wheat and maize, advancing systematic approaches in rice will help to improve the agronomic traits of other crop plants. For instance, NGS based genome-wide association studies (GWAS) have improved the resolution of quantitative trait loci (QTL) mapping in progenies of biparental crosses (Han and Huang 2013 Wang et al. 2016), systemic breeding is being based on modeling (Hammer et al. 2006 Lavarenne et al. 2018), and synthetic biology is being used for crop improvement (de Lange et al. 2018).

The data underlying systems biology are growing explosively (Stephens et al. 2015). To manage those big data efficiently, around 4800 databases have been generated (Wren et al. 2017). Many systems biology resources and well-reviewed research in rice are available (Chandran and Jung 2014 Garg and Jaiswal 2016 Li et al. 2018). However, given the proliferation, development, and updates of databases (Ősz et al. 2017 Imker 2018), an up-to-date review of the research infrastructure is essential. In this review, we report the development of tools and databases and classify them according to their major contributions to systems biology in rice. We also discuss the use of the resources and directions for further breeding and applications.


Biodiversity Information Serving Our Nation (BISON) - North American species occurrence data & maps Explore & download North American species occurrence data & maps

USGS Biodiversity Information Serving Our Nation (BISON) is a unique, web-based Federal mapping resource for species occurrence data in the United States and its Territories and Canada, including marine Exclusive Economic Zones (EEZs).

BISON Contributions to GBIF

The United States Geological Survey (USGS) hosts and administers the U.S. Node (GBIF-USA) of the Global Biodiversity Information Facility (GBIF), with the Biodiversity Information Serving Our Nation (BISON) project as one contribution to the Node's biodiversity informatics network. BISON provides a specialized publicly-accessible view of GBIF records for the U.S., U.S. Territories, Canada, and U.S. and Canadian marine Exclusive Economic Zones (EEZs), and assists with mobilization of U.S., U.S. Territorial, and Canadian species occurrence records to GBIF via the BISON instance of the GBIF Integrated Publishing Toolkit (IPT). The BISON instance of the GBIF IPT also provides public access to detailed metadata records for each dataset that has been made available through BISON by the BISON Data Team and its partners. BISON has a unique niche in the GBIF community by focusing on U.S. Government collections, invasive species data, and pollinator data for inclusion into GBIF.

Please send any comments, questions, errors or bugs encountered to [email protected]

Data Licensing and Value Added Fields

Data provided through Biodiversity Information Serving Our Nation (BISON) can be freely downloaded by users, however, restrictions for its use may vary with different data owners and is described at the record level upon download.

Data licensing is according to Creative Commons, and may commonly be: CC0 1.0 Universal, CC-BY 4.0 International, or CC-BY-NC 4.0 NonCommercial International. It is the responsibility of you, the user, to understand and obey the data licensing for all data you obtain from the BISON website.

The data is owned by the entity described in the OrganizationCode field and has been modified by BISON to provide some additional information, such as ITISscientificName, ITIScommonName, ITIStsn, validAcceptedITIStsn, computedCountyFips, calculatedCounty, calculatedState, mrgid, calculated_waterbody, and/or (if centroid=YES), decimalLatitude, decimalLongitude.

Note:
Maritime Boundaries (EEZ) geospatial data obtained from Marine Regions is licensed under the CC BY-NC-SA 4.0 NonCommercial ShareAlike International license. The vertices of this geospatial data have been simplified to match the scale of other data used in the BISON application.


Background

Ginseng (Panax ginseng C.A. Meyer) is a perennial herb of the Panax genus in Araliaceae family and has widely been used as a traditional medicine in Eastern Asia and North America. The principle bioactive components in ginseng are ginsenosides (collectively a group of triterpene saponins), which are biosynthesized through the isoprenoid pathway [1]. Ginseng has various therapeutic effects on humans including for treatment of cancer, diabetes, cardiovascular and stress [2,3,4,5,6]. P. ginseng is known to be tetraploid (2n = 4× = 48), with an estimated genome size of approximately 3.6 Gbp [7, 8]. Its large, highly repetitive genome, which has experienced whole-genome duplication, has impeded the progress of whole-genome sequencing of P. ginseng [7]. In addition, the long generation time (4 years) and difficulty of maintenance in ginseng cultivation fields have limited the genetic study of P. ginseng. Nevertheless, with the advent of new sequencing technologies, expressed sequence tags (ESTs) and RNA-Seq data have been generated from various tissues and growth stages of P. ginseng [9,10,11,12], based on which a number of genes involved in ginsenoside biosynthesis pathway have been characterized [10, 11]. Recently, the complete chloroplast genome sequences of P. ginseng cultivars and related species were characterized [13, 14]. Furthermore, inter- and intra-species chloroplast genome diversity were also identified for authentication of ginseng cultivars and species [13,14,15,16,17].

At the outset of this project, a total of 17,773 ESTs from NCBI db-EST (as of January, 2017) and a database for adventitious root [9] were publicly available for ginseng. However, these data were insufficient to facilitate the functional and comparative genomics and molecular breeding of ginseng. There was no comprehensive database publicly available for ginseng despite its importance as a medicinal crop with high pharmacological value. Given the fact that ginseng shows numerous effects on human health, a genomic and transcriptomic database is vital for ginseng research communities and other close relatives in the Apiales order. It is also anticipated that an integrated database of genetic, genomic, and metabolomic resources of ginseng would serve as a valuable resource for translational genomics. Recently, we generated extensive genomic and transcriptomic data for P. ginseng cultivar “Chunpoong” [18].

In this study, we built a dynamic database that integrates a draft genome sequence, transcriptome profiles, and annotation datasets of ginseng. This Ginseng Genome Database is now publicly available (http://ginsengdb.snu.ac.kr/) for the use of scientific community around the globe for exploring the vast possibilities.

This user-friendly database will serve as a hub for mining gene sequences and their digital expression data of samples from various tissues, developmental stages, and treatments. Our database interface will facilitate the easy retrieval of gene families and associated functional annotations using InterPro, KEGG, BLAST and Gene Ontology (GO) databases. To expedite metabolomics in ginseng, we have made a separate section that categorizes the genes associated with various metabolic pathways including the ginsenoside biosynthesis pathway. In addition, we have included robust tools such as BLAST and genome browser (JBrowse) [19] for survey and visualization of ginseng genomic features. This database will be updated regularly with new genome sequences and information on annotation and will provide reference genomic information for research in P. ginseng as well as related species.


Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.4571510.

Published by the Royal Society. All rights reserved.

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