In this issue

PubMed Abstract Plus

CD Tree and Cn3D Release

Whole Genome Shotgun Growth

New BLAST View Options

New Genome Builds–Map Viewer

New Organisms in UniGene

RefSeq Release 22

GenBank Release 158

NCBI Courses

Submissions Corner

PubChem Grows to 15 Million


New Genome Builds and Map Viewer Displays

New to Map Viewer

Genetic maps for twenty four new plants, the first assembled tree genome for black cottonwood (Populus trichocarpa), and two assembled protozoan parasite genomes are now available in the Map Viewer.

Plant Genetic Maps

The new plant genetic maps include important food and economic crops such as the common bean, Brassica oleracea—the source of cabbage, broccoli, cauliflower and Brussels sprouts—rye, rapeseed, cocoa, almond, and alfalfa. Also added are maps of close relatives and probable wild ancestors of some of these and other important crops. A complete list of the new plants with genetic maps can be found in Table 1. These genetic maps are important platforms for the future development of physical maps and complete genome sequences for several of these plants.

Genome Sequences

The Map Viewer now hosts the black cottonwood (Populus trichocarpa) genome assembly. This is the first woody plant genome assembly. The black cottonwood genome build 2.1 is the Joint Genome Institute's assembly of the 7.5 X whole genome shotgun sequence. Available sequence maps include NCBI contigs (the "Contig" map), the WGS sequences (the "Component" map), and the alignment of black cottonwood RNA sequences (the "PthRNA" map), UniGene clusters (the "PthUniGene" map), and Gnomon predicted gene models (the "ab-intio" map). The black cottonwood is not only an important experimental model species but is an economically important forestry resource. The poplar genome is well suited to serve as basis for comparative genomic studies of other broad leaf forest trees. Analysis of this genome has already provided important insights into the evolution of this group of plants into trees.

The genome assemblies and annotations for Trypanosoma brucei, the causative agent of African sleeping sickness, and Theileria parva, the causative agent of east coast fever—an African cattle disease, can now be viewed and searched in the map viewer.

The Theileria genome is based on a chromosome-by-chromosome whole genome assembly produced by The Institute for Genomic Research (TIGR) and the International Livestock Research Institute. The sequence is anchored to the four Theileria chromosomes. The current annotation contains 4,089 genes and their predicted transcripts. Theileria belongs to the Apicomplexa an important group of human and animal pathogens that includes the malaria parasites (Plasmodium). The Theileria genome now joins two other Apicomplexan genomes, Plasmodium falciparum and Cryptosporidium parvum, in the Map Viewer. Comparative analysis of these genomes will continue to provide insights into the parasite life cycles, host-parasite interactions and potential drug and vaccine targets.

The Trypanosoma genome is the assembly and annotation produced by an international consortium that includes the Sanger Center and TIGR. The sequence is of the eleven large chromosomes and does not include smaller mini and intermediate chromosomes. The mapped sequence and annotation represent 10,252 genes and their transcripts. The T. brucei genome is the first trypanosome genome in the Map Viewer. The sequencing and analysis of the genomes of T. cruzi, the causative agent of chagas disease and Leishmania major, responsible for leishmaniasis, together with the T. brucei genome should provide insights into the biology of these parasites that will help combat these diseases.

Other access to data

In addition to access through the Map Viewer, access to sequences of the genome assemblies, transcripts, proteins and gene models for black cottonwood, Theleiria parva and Trypanosoma brucei is provided through the RefSeq and Gene databases. GenBank and RefSeq records are available for searching in Entrez or via NCBI's Web BLAST services where they are extensively integrated with other resources and databases.

New Plant Species in Map Viewer

Aegilops tauschii
Aegilops umbellulata
Allium cepa
Brassica juncea
(Indian mustard)
Brassica napus
(oilseed rape)
Brassica Nigra
(black mustard)
Brassica oleracea
(cabbage and others)
Brassica rapa
(field mustard)
Capsicum annuum
(cayenne pepper)
Eragrostis tef
Medicago sativa
Phaseolus vulgaris
(French bean)
Populus trichocarpa
(black cottonwood)
Prunus dulcis
Secale cereale
Setaria italica
(foxtail millet)
Solanum lycopersicoides
Solanum melongena
Solanum peruvianum
(Peruvian tomato)
Sorghum bicolor
Theobroma cacao
Triticum turgidum
(English wheat)
Vigna radiata
(mung bean)
Table 1. New Plants with genetic maps in Map Viewer.

back to previous articleContinue to next article

NCBI News | Fall/Winter 2002 NCBI News: Spring 2003