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Pteris Genomics

    Participantspteris-vittata.jpg

    • Jody Banks
    • Michael Gribskov
    • Nadia Atallah
    • Alyssa Deleon
    • Qiong Wu
    • Yun Kim

    Weekly Meeting

    TBA every other sunday

    Links

    Overview

    A group devoted to the genomics of Pteris Vittata.

     

    Papers

    Xie QE, Yan XL, Liao XY, Li X. The arsenic hyperaccumulator fern Pteris vittata L. Environ Sci Technol. 2009 Nov 15;43(22):8488-95. doi: 10.1021/es9014647. PubMed PMID: 20028042. PDF

    Indriolo E, Na G, Ellis D, Salt DE, Banks JA. A Vacuolar Arsenite Transporter Necessary for Arsenic Tolerance in the Arsenic Hyperaccumulating Fern Pteris vittata Is Missing in Flowering Plants.  Plant Cell 22, 2045–2057,2010. PDF
     
    Ellis DR, Gumaelius L, Indriolo E, Pickering IJ, Banks JA, Salt DE. A novel arsenate reductase from the arsenic hyperaccumulating fern Pteris vittata. Plant  Physiol. 2006 Aug;141(4):1544-54. Epub 2006 Jun 9. PubMed PMID: 16766666; PubMed  Central PMCID: PMC1533930.
     
    Su YH, McGrath SP, Zhu YG, Zhao FJ. Highly efficient xylem transport of arsenite in the arsenic hyperaccumulator Pteris vittata. New Phytol. 2008;180(2):434-41. doi: 10.1111/j.1469-8137.2008.02584.x. Epub 2008 Jul 25. PubMed PMID: 18662326.
     
    Pickering IJ, Gumaelius L, Harris HH, Prince RC, Hirsch G, Banks JA, Salt DE, George GN. Localizing the biochemical transformations of arsenate in a hyperaccumulating fern. Environ Sci Technol. 2006 Aug 15;40(16):5010-4. PubMed PMID: 16955900.
     

    Gumaelius L, Lahner B, Salt DE, Banks JA. Arsenic hyperaccumulation in gametophytes of Pteris vittata. A new model system for analysis of arsenic hyperaccumulation. Plant Physiol. 2004 Oct;136(2):3198-208. Epub 2004 Sep 24. PubMed PMID: 15448194; PubMed Central PMCID: PMC523379.

    Webb SM, Gaillard JF, Ma LQ, Tu C. XAS speciation of arsenic in a hyper-accumulating fern. Environ Sci Technol. 2003 Feb 15;37(4):754-60. PubMed PMID: 12636275.

    Arsenic Induced Differential Gene Expression

    comp98614, glutathione S-transferase

    • 232 fold up-regulated in RNASeq
      1 subcomponent, 3 sequences
      AT2G30870.1  215   1  208  210  49.52  8.00E-64  ATGSTF10, ERD13, ATGSTF4, GSTF10| glutathione S-transferase PHI 10 | chr2:13141490-13142392
      AT3G03190.1  214   1  213  214  45.33  1.00E-63  ATGSTF11, ATGSTF6, GSTF11       | glutathione S-transferase F11 | chr3:735071-735877
      AT2G30860.1  215   1  204  206  49.51  9.00E-62  ATGSTF9, GLUTTR, ATGSTF7, GSTF9 | glutathione S-transferase PHI 9 | chr2:13139132-13140057
               .2  166   1  155  157  47.77  4.00E-40  ATGSTF9, GLUTTR, ATGSTF7, GSTF9 | glutathione S-transferase PHI 9 | chr2:13139132-13140079
      AT5G17220.1  214   1  212  213  42.25  2.00E-53  ATGSTF12, GST26, TT19, GSTF12   | glutathione S-transferase phi 12 | chr5:5658528-5659322
      AT3G62760.1  219   1  209  211  42.18  2.00E-52  ATGSTF13                        | Glutathione S-transferase family protein | chr3:23217425-23218246
      AT2G47730.1  263  54  260  209  45.45  3.00E-51  ATGSTF8, ATGSTF5, GST6, GSTF8   | glutathione S-transferase phi 8 | chr2:19558213-19559266
      GST Phi 10 AKA Early Response to Dehydration (ERD) 13
      Top three are equivalent, full length matches
    • More Information

     

    comp108897, Transposon reverse transcriptase

    • 13.2 fold upregulated in RNASeq

      AT4G23160.1  37.19  242  146  3  1383  2102  67  304  2e-44  172     CRK8 | cysteine-rich RLK (RECEPTOR-like protein kinase) 8 | chr4:12129485-12134086
      ATMG00820.1  44.09   93   50  1  1485  1763  42  132  6e-18   83.6 ORF170 | Reverse transcriptase (RNA-dependent DNA polymerase) | chrM:228573-229085
      covers only 250 residues of the CRLK8 recptor (1262 residues), so probably not CRLK.  In some of the results (not show) up to 198 of 240 residues of ORF170 are covered.
    • More Information

    comp103624, 4-Oct organic cation tranporter

    • 48.4 fold up-regulated in RNASeq
    • comp103624_c0_seq1  AT3G20660.1  40.15  523  285   7  40  1575  5  510  2e-119   370  AtOCT4, 4-Oct | organic cation/carnitine transporter4
                                                                                                          |  chr3:7225271-7228510
    • More Information
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    Files 9

    FileSizeDateAttached by 
     deseq.pdf
    DESeq
    753.77 kB11:06, 25 Jun 2012wu41Actions
     edger.pdf
    edgeR
    128.02 kB11:06, 25 Jun 2012wu41Actions
     Experimental methods for Pteris vittata genomics project.doc
    No description
    27.5 kB15:14, 22 Mar 2012deleon0Actions
     Pickering 2006.pdf
    No description
    328.08 kB10:19, 8 Mar 2012banksjActions
     Plant Physiol.-2004.pdf
    Plant Phys. 2004
    409.5 kB10:18, 8 Mar 2012banksjActions
     Plant Physiol.-2006.pdf
    No description
    325.59 kB10:21, 8 Mar 2012banksjActions
     pteris-vittata.jpg
    No description
    130.22 kB13:48, 7 Mar 2012gribskovActions
     RSEM.pdf
    No description
    469.9 kB21:55, 16 Mar 2012natallahActions
     TrinityRSEM_script
    The scripts Nadia used in RNAseq analysis of Ceratopteris using Trinity and RSEMv1.1.13
    1333 bytes21:53, 16 Mar 2012natallahActions
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