Nectria haematococca v2.0

Status

v.2.0 (March 5, 2007): Chromosomes are numbered based on the Optical map (April 2006). 92.26% of the sequence is mapped to chromosomes. The remaining 7.74% of sequence remains unmapped. All mapped and unmapped sequence is contained in the Nectria_version2release_062706.fasta file.

All available ESTs (41,472 clones representing 20,736 cDNA clones) were placed on the finished assembly. All ESTS with high quality sequence traces were found except 4 (CATN121-L22, CATN13-C10, CATN77-A17, CAUA05-M04.) One thing to note is there does appear to be a high percentage of chimeric clones in these cDNA libraries.

Chromosome
SHGC_ID
# Scaffolds
Size
Comment
1
5300
3
6,369,736
-
2
5303
2
4,350,924
-
3
5301
6
4,591,189
-
4
5302
4
4,237,857
*
5
5304
3
3,973,246
-
6
5306
4
3,621,839
-
7
5308
11
2,948,412
-
8
5309
3
3,391,797
-
9
5305
2
3,013,008
-
10
5312
4
2,731,896
-
11
5325
7
2,284,780
-
12
5314
5
2,325,368
-
13
5323
6
1,298,360
*
14
5320
5
1,260,466
-
15
5366
3
346,570
-
16
5367
1
215,166
*
17
5368
3
230,523
*

Size of mapped scaffolds: 47,191.137bp
Size of unmapped scaffolds: 3,958.438bp
TOTAL GENOME SIZE: 51,149.575bp

* = telomere present

Note on scaffold nomenclature: Scaffold names have the form sca_[scaffold #]_chr[chromosome #]_[relative position of scaffold in chromosome]_[number to allow mapping of future scaffolds to intermediate positions]

The current annotation release, version 2.0, includes a total of 15,707 gene models predicted and functionally annotated using the JGI annotation pipeline. In addition, manual curations of 883 gene models in version 1.0 were transferred to version 2.0.

Collaborators

Links

References

Jeffrey J. Coleman Steve D. Rounsley, Marianela Rodriguez-Carres1, Alan Kuo, Catherine C. Wasmann, Jane Grimwood, Jeremy Schmutz, Masatoki Taga, Gerard J. White1, Shiguo Zhou, David C. Schwartz, Michael Freitag, Li-jun Ma11, Etienne G. J. Danchin, Bernard Henrissat, Pedro M. Coutinho, David R. Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. Barker, Michael Gribskov, Scott Kroken, István Molnár, Christopher Rensing, John C. Kennell, Jorge Zamora1, Mark L. Farman, Eric U. Selker, Asaf Salamof, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Casey Lamers, Igor V. Grigoriev, David M. Geiser, Sarah F. Covert, Esteban Temporini1, Hans D. VanEtten1,Martijn Rep The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion PLoS Genetics , August 2009

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.