Reading PAGE

Peer Evaluation activity

Downloads 3
Views 41
Full text requests 2

Total impact ?

    Send a

    Ahmed has...

    Trusted 0
    Reviewed 0
    Emailed 0
    Shared/re-used 0
    Discussed 0
    Invited 0
    Collected 0

     

    This was brought to you by:

    block this user Ahmed Moustafa

    Assistant Professor

    American University in Cairo

    A phylogenomic approach for studying plastid endosymbiosis.

    Export to Mendeley

    Gene transfer is a major contributing factor to functional innovation in genomes. Endosymbiotic gene transfer (EGT) is a specific instance of lateral gene transfer (LGT) in which genetic materials are acquired by the host genome from an endosymbiont that has been engulfed and retained in the cytoplasm. Here we present a comprehensive approach for detecting gene transfer within a phylogenetic framework. We applied the approach to examine EGT of red algal genes into Thalassiosira pseudonana, a free-living diatom for which a complete genome sequence has recently been determined. Out of 11,390 predicted protein-coding sequences from the genome of T. pseudonana, 124 (1.1%, clustered into 80 gene families) are inferred to be of red algal origin (bootstrap support >or= 75%). Of these 80 gene families, 22 (27.5%) encode novel, unknown functions. We found 21.3% of the gene families to putatively encode non-plastid-targeted proteins. Our results suggest that EGT of red algal genes provides a relatively minor contribution to the nuclear genome of the diatom, but the transferred genes have functions that extend beyond photosynthesis. This assertion awaits experimental validation. Whereas the current study is focused within the context of secondary endosymbiosis, our approach can be applied to large-scale detection of gene transfer in any system.

    Oh la laClose

    Your session has expired but don’t worry, your message
    has been saved.Please log in and we’ll bring you back
    to this page. You’ll just need to click “Send”.

    Your evaluation is of great value to our authors and readers. Many thanks for your time.

    Review Close

    Short review
    Select a comment
    Select a grade
    You and the author
    Anonymity My review is anonymous( Log in  or  Register )
    publish
    Close

    When you're done, click "publish"

    Only blue fields are mandatory.

    Relation to the author*
    Overall Comment*
    Anonymity* My review is anonymous( Log in  or  Register )
     

    Focus & Objectives*

    Have the objectives and the central topic been clearly introduced?

    Novelty & Originality*

    Do you consider this work to be an interesting contribution to knowledge?

    Arrangement, Transition and Logic

    Are the different sections of this work well arranged and distributed?

    Methodology & Results

    Is the author's methodology relevant to both the objectives and the results?

    Data Settings & Figures

    Were tables and figures appropriate and well conceived?

    References and bibliography

    Is this work well documented and has the bibliography been properly established?

    Writing

    Is this work well written, checked and edited?

    Write Your Review (you can paste text as well)
    Please be civil and constructive. Thank you.


    Grade (optional, N/A by default)

    N/A 1 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 8 8.5 9 9.5 10
    Close

    Your mailing list is currently empty.
    It will build up as you send messages
    and links to your peers.

     No one besides you has access to this list.
    Close
    Enter the e-mail addresses of your recipients in the box below.  Note: Peer Evaluation will NOT store these email addresses   log in
    Your recipients

    Your message:

    Your email : Your email address will not be stored or shared with others.

    Your message has been sent.

    Description

    Title : A phylogenomic approach for studying plastid endosymbiosis.
    Author(s) : Ahmed Moustafa, Cheong Xin Chan, Megan Danforth, David Zear, Hiba Ahmed, Nagnath Jadhav, Trevor Savage, Debashish Bhattacharya
    Abstract : Gene transfer is a major contributing factor to functional innovation in genomes. Endosymbiotic gene transfer (EGT) is a specific instance of lateral gene transfer (LGT) in which genetic materials are acquired by the host genome from an endosymbiont that has been engulfed and retained in the cytoplasm. Here we present a comprehensive approach for detecting gene transfer within a phylogenetic framework. We applied the approach to examine EGT of red algal genes into Thalassiosira pseudonana, a free-living diatom for which a complete genome sequence has recently been determined. Out of 11,390 predicted protein-coding sequences from the genome of T. pseudonana, 124 (1.1%, clustered into 80 gene families) are inferred to be of red algal origin (bootstrap support >or= 75%). Of these 80 gene families, 22 (27.5%) encode novel, unknown functions. We found 21.3% of the gene families to putatively encode non-plastid-targeted proteins. Our results suggest that EGT of red algal genes provides a relatively minor contribution to the nuclear genome of the diatom, but the transferred genes have functions that extend beyond photosynthesis. This assertion awaits experimental validation. Whereas the current study is focused within the context of secondary endosymbiosis, our approach can be applied to large-scale detection of gene transfer in any system.
    Subject : unspecified
    Area : Other
    Language : English
    Year : 2008

    Affiliations American University in Cairo
    Journal : Genome informatics International Conference on Genome Informatic
    Volume : 21
    Pages : 165-176
    Url : http://www.ncbi.nlm.nih.gov/pubmed/19425156

    Leave a comment

    This contribution has not been reviewed yet. review?

    You may receive the Trusted member label after :

    • Reviewing 10 uploads, whatever the media type.
    • Being trusted by 10 peers.
    • If you are blocked by 10 peers the "Trust label" will be suspended from your page. We encourage you to contact the administrator to contest the suspension.

    Does this seem fair to you? Please make your suggestions.

    Please select an affiliation to sign your evaluation:

    Cancel Evaluation Save

    Please select an affiliation:

    Cancel   Save

    Ahmed's Peer Evaluation activity

    Downloads 3
    Views 41
    Full text requests 2

    Ahmed has...

    Trusted 0
    Reviewed 0
    Emailed 0
    Shared/re-used 0
    Discussed 0
    Invited 0
    Collected 0
    Invite this peer to...
    Title
    Start date (dd/mm/aaaa)
    Location
    URL
    Message
    send
    Close

    Full Text request

    Your request will be sent.

    Please enter your email address to be notified
    when this article becomes available

    Your email


     
    Your email address will not be shared or spammed.