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  • List of Plant whose Genome Assembly has been done

    Dear All,

    Is there any list or Database from where I can find out the names of the Plants whose genome assembly has been done.

    I did a PubMed search but wanted a more comprehensive list.(same for SRA)

    Thanking you,
    Prakhar Gaur

  • #2
    Originally posted by gprakhar View Post
    Dear All,

    Is there any list or Database from where I can find out the names of the Plants whose genome assembly has been done.

    I did a PubMed search but wanted a more comprehensive list.(same for SRA)

    Thanking you,
    Prakhar Gaur
    NCBI Taxobrowser will give you all available genome sequences for Plants. It does include Chloroplast and Mitochondrial sequences but those can easily be removed

    This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.

    Comment


    • #3
      Originally posted by jimmybee View Post
      NCBI Taxobrowser will give you all available genome sequences for Plants. It does include Chloroplast and Mitochondrial sequences but those can easily be removed

      http://www.ncbi.nlm.nih.gov/genome/?...[Organism:exp]
      Thanks for the reply.

      This will only tell about the organisms whose Genome is available.
      I want to know about the Plants whose Genome assembly has been done using NGS technologies.
      Its a kind of Literature survey work I am doing as I have to chalk out our own strategy regarding this.

      Have already done PubMed searches, but asking here just to be sure.

      --
      pg
      Last edited by gprakhar; 08-05-2011, 12:59 AM. Reason: grammar

      Comment


      • #4
        You might get some more info on the GOLD Genomes online database.

        Comment


        • #5
          Post your list

          Originally posted by gprakhar View Post
          Dear All,

          Is there any list or Database from where I can find out the names of the Plants whose genome assembly has been done.

          I did a PubMed search but wanted a more comprehensive list.(same for SRA)

          Thanking you,
          Prakhar Gaur
          Dear Prakhar,
          Could you post your list here when you've completed it? Thanks.

          Comment


          • #6
            Two useful places to check for this might be the JGI:



            and the BMAP consortium (for the brassicaceae):

            Comment


            • #7
              Originally posted by colindaven View Post
              You might get some more info on the GOLD Genomes online database.
              Thank you for the suggestion.
              I checked out the GOLD db, but it does not contain the kind of data I am looking for.(update by groups who did want their data to be there)
              Additionally it looks like it has not been updated for a long time.


              Regards,
              --
              pg

              Comment


              • #8
                Originally posted by plattsa View Post
                Two useful places to check for this might be the JGI:



                and the BMAP consortium (for the brassicaceae):

                http://www.brassica.info/resource/sequencing/bmap.php
                Thank you for the reply,
                JGI provided lots of info and so did BMAP(only about the Brassicaceae family though)

                Regards,
                --
                pg

                Comment


                • #9
                  Originally posted by Joann View Post
                  Dear Prakhar,
                  Could you post your list here when you've completed it? Thanks.
                  Yes sure.

                  I have given up hope of finding a comprehensive list of Plants genomes sequenced using NGS technology.

                  And have decided to make one myself.
                  Only one question to the Admin, can we have a wiki like list for this???
                  As in a separate page for the list!
                  That way I will populate the list initially and then everyone can contribute.
                  A similar thing for others(eg. vertebrates) will also do good for the community.

                  --
                  pg

                  Comment


                  • #10
                    I personally found this list very helpful:



                    Best wishes!

                    Comment


                    • #11
                      I've been expanding this page, but is it complete?



                      Thanks for any feedback or edits,
                      Homepage: Dan Bolser
                      MetaBase the database of biological databases.

                      Comment


                      • #12
                        We've recently published some 'partially' assembled crucifer genomes (scaffolds go up to 16MBase) and there may be a couple of other published genomes used in the paper as well that you may/may-not not have:

                        Comment


                        • #13
                          Originally posted by dan View Post
                          I've been expanding this page, but is it complete?



                          Thanks for any feedback or edits,
                          A good number of those genomes have not been assembled or annotated. You'll probably need to either redefined what you have suggested as a sequenced genome. Currently the page says "This list of sequenced plant genomes contains plant species known to have publicly available complete genome sequences that have been assembled, annotated and published. Unassembled genomes are not included, nor are organelle only sequences".

                          Maybe you should add a column with the relative "completeness" of each genome? E.g. Rice is quite complete (assembled into chromosome pseudomolecules, annotated well etc, whereas the Triticum species have little annotation and have not been assembled into anything like a chromosome).

                          Otherwise this is a great resource. Thanks for updating

                          Comment


                          • #14
                            Originally posted by jimmybee View Post
                            Maybe you should add a column with the relative "completeness" of each genome? E.g. Rice is quite complete (assembled into chromosome pseudomolecules, annotated well etc, whereas the Triticum species have little annotation and have not been assembled into anything like a chromosome).
                            Absolutely agree. Actually that was my original intention when I started work on this page, but I got side-tracked ;-)

                            If I add the column, will you help populate the data? I figure we should use the standards linked here:


                            Many thanks,
                            Homepage: Dan Bolser
                            MetaBase the database of biological databases.

                            Comment


                            • #15
                              Originally posted by dan View Post
                              Absolutely agree. Actually that was my original intention when I started work on this page, but I got side-tracked ;-)

                              If I add the column, will you help populate the data? I figure we should use the standards linked here:


                              Many thanks,
                              Absolutely. I'll populate some info tonight

                              Comment

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