Genome Assembly/V1.1

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Contamination filtered 8x assembly that was the basis for the initial publication and is submitted to Genbank:

LOCUS       ABEU01000000           19135 rc    DNA     linear   PLN 24-JAN-2008
DEFINITION  Physcomitrella patens subsp. patens whole genome shotgun sequencing
            project.
ACCESSION   ABEU00000000
VERSION     ABEU00000000.1  GI:161158655
PROJECT     GenomeProject:13064
KEYWORDS    WGS.
SOURCE      Physcomitrella patens subsp. patens
  ORGANISM  Physcomitrella patens subsp. patens
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta;
            Moss Superclass V; Bryopsida; Funariidae; Funariales; Funariaceae;
            Physcomitrella.
REFERENCE   1  (bases 1 to 19135)
  AUTHORS   Rensing,S.A., Lang,D., Zimmer,A.D., Terry,A., Salamov,A.,
            Shapiro,H., Nishiyama,T., Perroud,P.F., Lindquist,E.A.,
            Kamisugi,Y., Tanahashi,T., Sakakibara,K., Fujita,T., Oishi,K.,
            Shin-I,T., Kuroki,Y., Toyoda,A., Suzuki,Y., Hashimoto,S.,
            Yamaguchi,K., Sugano,S., Kohara,Y., Fujiyama,A., Anterola,A.,
            Aoki,S., Ashton,N., Barbazuk,W.B., Barker,E., Bennetzen,J.L.,
            Blankenship,R., Cho,S.H., Dutcher,S.K., Estelle,M., Fawcett,J.A.,
            Gundlach,H., Hanada,K., Heyl,A., Hicks,K.A., Hughes,J., Lohr,M.,
            Mayer,K., Melkozernov,A., Murata,T., Nelson,D.R., Pils,B.,
            Prigge,M., Reiss,B., Renner,T., Rombauts,S., Rushton,P.J.,
            Sanderfoot,A., Schween,G., Shiu,S.H., Stueber,K., Theodoulou,F.L.,
            Tu,H., Van de Peer,Y., Verrier,P.J., Waters,E., Wood,A., Yang,L.,
            Cove,D., Cuming,A.C., Hasebe,M., Lucas,S., Mishler,B.D., Reski,R.,
            Grigoriev,I.V., Quatrano,R.S. and Boore,J.L.
  TITLE     The Physcomitrella genome reveals evolutionary insights into the
            conquest of land by plants
  JOURNAL   Science 319 (5859), 64-69 (2008)
   PUBMED   18079367
REFERENCE   2  (bases 1 to 19135)
  AUTHORS   Terry,A., Salamov,A., Zhou,K., Pitluck,S., Lucas,S., Detter,J.C.,
            Glavina del Rio,T., Shapiro,H., Tu,H., Lindquist,E., Anterola,A.,
            Ashton,N., Barker,E., Cuming,A., Dutcher,S., Engelken,J.,
            Hughes,J., Lang,D., Ma,S., Merchant,S., Napoli,C., Roberts,A.,
            Rushton,P., Sanderfoot,T., Verrier,P., Wood,A., Rensing,S.,
            Quatrano,R.S., Grigoriev,I. and Boore,J.L.
  CONSRTM   US DOE Joint Genome Institute (JGI-PGF)
  TITLE     Direct Submission
  JOURNAL   Submitted (15-NOV-2007) US DOE Joint Genome Institute, 2800
            Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
COMMENT     The Physcomitrella patens subsp. patens whole genome shotgun (WGS)
            project has the project accession ABEU00000000.  This version of
            the project (01) has the accession number ABEU01000000, and
            consists of sequences ABEU01000001-ABEU01019135.
            URL -- http://www.jgi.doe.gov/Physcomitrella
            JGI Project ID: 3640246
            Source DNA and stock culture is available from Ralph Quatrano
            (rsq@wustl.edu)
            Contacts: Ralph Quatrano (rsq@biology2.wustl.edu)
                      Jeff Boore (jlboore@calmail.berkeley.edu)
            Annotation done by JGI-PGF and the Physcomitrella patens Consortium
            The JGI and collaborators endorse the principles for the
            distribution and use of large scale sequencing data adopted by the
            larger genome sequencing community and urge users of this data to
            follow them. It is our intention to publish the work of this
            project in a timely fashion and we welcome collaborative
            interaction on the project and analysis.
            (http://www.genome.gov/page.cfm?pageID=10506376)
            This version of the project, V1.1, represents 8.1x coverage of the
            genome.
FEATURES             Location/Qualifiers
     source          1..19135
                     /organism="Physcomitrella patens subsp. patens"
                     /mol_type="genomic DNA"
                     /sub_species="patens"
                     /db_xref="taxon:145481"
                     /ecotype="Gransden 2004"
WGS         ABEU01000001-ABEU01019135
WGS_SCAFLD  DS544890-DS546995
//

Additional contaminations still present

scaffold_1419
Evidence:HR gene tree cluster 81 (2 gene models without real exons: Phypa_157595,Phypa_157599) --DanDaMan 08:56, 19 June 2007 (CEST)
scaffold_1840
Evidence:HR gene tree cluster 81 (2 gene models without real exons: Phypa_103316,Phypa_103317) --DanDaMan 08:56, 19 June 2007 (CEST)
scaffold_11199
Evidence:T-box leader from gram-positive bacteria scaffold_11199:786..1024 --DanDaMan 17:10, 5 October 2007 (CEST)
scaffold_1290
Evidence:T-box leader from gram-positive bacteria gbrowse_pp:scaffold_1290:3782..4024 --DanDaMan 17:51, 5 October 2007 (CEST)
scaffold_9388
Evidence:T-box leader from gram-positive bacteria gbrowse_pp:scaffold_9388:749..978 --DanDaMan 17:51, 5 October 2007 (CEST)
scaffold_1340
Evidence:ydaO/YuaA leader is a conserved RNA structure found upstream of the ydaO and yuaA genes in Bacillus subtilis and related genes in other bacteria. gbrowse_pp:scaffold_1340:8883..9044
scaffold_2138
Whole scaffold only consists of clear bacterial intron-less/low genes gbrowse_pp:scaffold_2138
scaffold_11218
Probably part of the Bacillus contamination e.g. ~40% identity to ZP_01721818 methyl-accepting chemotaxis protein [Bacillus sp. B14905]. gbrowse_pp:scaffold_11218
scaffold_3671
Plate switch contaminant 'Delftia acidovorans genome CP000884 gbrowse_pp:scaffold_3671

The scaffolds are removed from Genome_Assembly/V1.2.

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