Bonjour,

Suite à la correction de notre séquence, nous rencontrons un problème avec nos arbres:

Nous avons un problème pour classer notre séquence dans une catégorie.
Notre séquence à de fortes homologies avec des alpha-protéo et des eucaryotes. De plus, le domaine protéique est:"Stabilizer of iron transporter SufD", impliqué dans le transport du fer. On s'attend donc à retrouver notre séquence dans des bactéries à l'origine de mitochondrie ou chloroplaste.

Notre arbre avec la méthode parcimonie est abhérent (arbre a). Notre arbre par NJ (arbre b) nous donne la séquence dans les CFB bactéries.
Nous avons suivi les conseils de madame Brochier, nous avons fait des arbres non racinés avec plus de séquences de bactéries ( arbre c par parcimonie et arbre d par NJ). Ils sont totalement incohérents.
Monsieur Hingamp nous a dit de faire un arbre avec la méthode phyML qui donne encore quelque chose de différent: elle est proche des alpha-protéo (arbre e).

Nous avons vérifié avec M. Hingamp la validité des alignements multiples, surtout pour le groupe exterieur (les archées), qui semble bonne.

Mme Brochier nous a dit connaitre la séquence étudiée, pourrions-nous avoir des pistes de recherche ?

Cordialement

a)                                                                           +------Fbacterium2    [CFB group bacteria]
                                                                        +--1.0-|
                                                                 +--1.0-|      +------Fbacterium1   [CFB group bacteria]
                                                                 |      |
                                                          +--1.0-|      +-------------tenacibaculum    [CFB group bacteria]
                                                          |      |
                                                          |      |      +-------------Aproteobact    [a-proteobacteria]
                                                          |      +--1.0-|
                                                          |             |      +------Fpelagi    [a-proteobacteria]
                                                          |             +--1.0-|
                                                   +--0.8-|                    +------Msilvestris    [a-proteobacteria]
                                                   |      |
                                                   |      |                    +------Kpneumoniae    [enterobacteria]
                                                   |      |             +--1.0-|
                                                   |      |      +--1.0-|      +------Ecoli     [enterobacteria]
                                            +--0.8-|      |      |      |
                                            |      |      +--0.8-|      +-------------salmonallaT     [enterobacteria]
                                            |      |             |
                                            |      |             +--------------------Xfastidiosa    [g-proteobacteria]
                                     +--0.5-|      |
                                     |      |      |                           +------CAPgenomovar   [CFB group bacteria]
                                     |      |      +-----------------------1.0-|
                                     |      |                                  +------Bfragilis    [CFB group bacteria]
                                     |      |
                              +--0.8-|      +-----------------------------------------Cburnetii    [g-proteobacteria]
                              |      |
                              |      |                                         +------synechococcus    [cyanobacteria]
                              |      |                           +---------1.0-|
                              |      |                           |             +------Pmarinus    [cyanobacteria]
                              |      +-----------------------1.0-|
                       +--0.8-|                                  |             +------Npunctiforme    [cyanobacteria]
                       |      |                                  |      +--1.0-|
                       |      |                                  +--1.0-|      +------Maeruginosa    [cyanobacteria]
                       |      |                                         |
                +--1.0-|      |                                         +-------------synechocystis    [cyanobacteria]
                |      |      |
                |      |      +-------------------------------------------------------polaromonas    
         +--1.0-|      |
         |      |      +--------------------------------------------------------------Bthailandensis    
         |      |
         |      |                                                              +------Tpendens    [crenarchaeotes]
  +------|      +----------------------------------------------------------0.8-|
  |      |                                                                     +------Npharaonis    [euryarchaeotes]
  |      |
  |      |                                                                     +------Mmaripaludis    [euryarchaeotes]
  |      +-----------------------------------------------------------------1.0-|
  |                                                                            +------SEQinconnue
  |
  +-----------------------------------------------------------------------------------Aboonei    [euryarchaeotes]


arbre b

                   +-----------Tpendens     [crenarchaeotes]  
                   !
                   !                   +Ecoli    [enterobacteria]    
                   !                 +-4
                   !          +------5 +Kpneumoniae     [enterobacteria]    
               +---3          !      !
               !   !          !      +-salmonallaT   [enterobacteria]  
               !   !          !  
               !   !          !          +SEQinconnue    
               !   !          !        +-6
               !   !          !     +--7 +-Fbacterium2    [CFB group bacteria]  
               !   +---------13     !  !
               !              !  +-10  +-Fbacterium1     [CFB group bacteria]  
               !              !  !  !  
               !              !  !  +---tenacibaculum     [CFB group bacteria]  
               !              !  !  
               !              !  !        +----Fpelagi  [a-proteobacteria]
    
               !              +-17     +-14  
               !                 !  +-15  +---Msilvestris   [a-proteobacteria]
    
               !                 !  !  !  
               !                 !  !  +----Aproteobact     [a-proteobacteria]
    
               !                 !  !  
               !                 !  !     +------Xfastidiosa    [g-proteobacteria]    
               !                 +-19  +-16  
  +------------2                    !  !  +------Bthailandensis    
    
  !            !                    !  !  
  !            !                    !  !             +-synechocystis    [cyanobacteria]    
  !            !                    !  !           +-9
  !            !                    +-20        +-11 +--Maeruginosa    [cyanobacteria]    
  !            !                       !        !  !  
  !            !                       !     +-12  +--Npunctiforme     [cyanobacteria]  
  !            !                       !     !  !  
  !            !                       !  +-18  +----synechococcus     [cyanobacteria]  
  !            !                       !  !  !  
  !            !                       +-21  +----Pmarinus      [cyanobacteria]
  !            !                          !  
  !            !                          !  +----Cburnetii     [g-proteobacteria]  
  !            !                          +-22  
  !            !                             !  +----polaromonas    
  
  !            !                             +-23  
  !            !                                !  +--Bfragilis    [CFB group bacteria]    
  !            !                                +--8
  !            !                                   +----------------CAPgenomovar    [CFB group bacteria]    
  !            !
  !            +---------------Npharaonis    [euryarchaeotes]    
  !
  1------------------------Aboonei   [euryarchaeotes]  
  !
  +---------------------------------------------------------Mmaripaludis    [euryarchaeotes]    


arbre c

        +-----------------------------------------------------SEQinconnue    
        |  
        |  +--------------------------------------------------Fjohnsoniae   [CFB group bacteria]
        |  |  
        |  |                                               +--Rhizobium    [a-proteobacteria]
     +-15  |                                         +----12  
     |  |  |                                         |     +--Mchloromethanicum    [a-proteobacteria]
     |  |  |                                   +----11  
     |  |  |                                   |     |     +--Roseobacter    [a-proteobacteria]
     |  |  |                                   |     +----13  
     |  +-14  +-------------------------------10           +--Gdiazotrophicus    [a-proteobacteria]
     |     |  |                                |  
     |     |  |                                |           +--Rrubrum    [a-proteobacteria]
     |     |  |                                +-----------9  
     |     |  |                                            +--Aproteo     [a-proteobacteria]
     |     |  |  
     |     |  |                                   +-----------CBlochmanniafloridanus    [enterobacteria]
     |     |  |                                +-20  
     |     |  |                                |  |  +--------Pluminescens    [enterobacteria]
     |     +--8                                |  +-19  
     |        |                                |     |  +-----Kpneunomonia    [enterobacteria]
  +--2        |                             +-16     +-18  
  |  |        |                             |  |        |  +--Ealbertii    [enterobacteria]
  |  |        |                             |  |        +-17  
  |  |        |                 +-----------7  |           +--Ecoli    [enterobacteria]
  |  |        |                 |           |  |  
  |  |        |                 |           |  +--------------Lyngbya     [cyanobacteria]
  |  |        |                 |           |  
  |  |        +-----------------6           +-----------------Bplebeius     [CFB group bacteria]
  |  |                          |  
  1  |                          |                          +--Gviolaceus   [cyanobacteria]  
  |  |                          |                    +-----5  
  |  |                          |                    |     +--Noceani     [g-proteobacteria]
  |  |                          +--------------------4  
  |  |                                               |     +--Saurantiaca     [d-proteobacteria]
  |  |                                               +-----3  
  |  |                                                     +--Anaeromyxobacter     [d-proteobacteria]
  |  |  
  |  +--------------------------------------------------------Marinomas     [g-proteobacteria]
  |  
  +-----------------------------------------------------------Cjaponicus     [g-proteobacteria]


arbre d



+------Marinomas  [g-proteobacteria]  
  !
  !      +-----------Fjohnsoniae    [CFB group bacteria]  
  !      !  
  !      !   +SEQinconnue    
  !   +-13   !
  !   !  !   !              +Ecoli    [enterobacteria]
  !   !  !   !            +-1
  !   !  +---6        +---2 +Ealbertii   [enterobacteria]
  !   !      !        !   !
  !   !      !     +--3   +-Kpneunomonia   [enterobacteria]  
  !   !      !     !  !
  !   !      +-----4  +----Pluminescens    [enterobacteria]  
  !   !            !
  !   !            +--------------CBlochmanniafloridanus    [enterobacteria]
  !   !  
  7--14           +-----Aproteo   [a-proteobacteria]  
  !   !        +-10  
  !   !     +-11  +-----Rrubrum   [a-proteobacteria]
  !   !     !  !  
  !   !     !  +--------Gdiazotrophicus    [a-proteobacteria]
  !   !  +-12  
  !   !  !  !    +-----Mchloromethanicum     [a-proteobacteria]
  !   !  !  ! +--5
  !   !  !  +-8  +----Rhizobium    [a-proteobacteria]
  !   !  !    !
  !   !  !    +-----------Roseobacter    [a-proteobacteria]
  !   +-15  
  !      !       +-----Anaeromyxobacter     [d-proteobacteria]
  !      !     +-9
  !      !     ! +-------Saurantiaca     [d-proteobacteria]
  !      !  +-17  
  !      !  !  !  +------Noceani     [g-proteobacteria]
  !      !  !  +-16  
  !      +-18     +------Gviolaceus     [cyanobacteria]
  !         !  
  !         !  +----------Bplebeius     [CFB group bacteria]
  !         +-19  
  !            +----------Lyngbya     [cyanobacteria]
  !
  +----Cjaponicus   [g-proteobacteria]  


arbre e


                                  +-------------------------------------------------------------------------Mmaripaludis
+--------------------------------+
|                                +----------------------------------------------------------Aboonei
|
|                         +------------------------------------------------------------Tpendens
|+------------------------+
||                        +-----------------------------------------Npharaonis
||
||
||                                                      +----Fpelagi
++                                                 +----+
  |                                                 |    +---------Msilvestris
  |                                                 |
  |                                                 |     +------------------------Bthailandensis
  |                                                 |     |
  +-------------------------------------------------+     |               +-----------CAPgenomovar
                                                    |     |         +-----+
                                                    |     |         |     +---Bfragilis
                                                    |     |         |
                                                    |     |  +------+      +---tenacibaculum
                                                    +-----+  |      |    +-+
                                                          |  |      |    | +---Fbacterium2
                                                          |  |      +----+
                                                          |  |           +Fbacterium1
                                                          |  |
                                                          |  |      +------Aproteobact
                                                          |  |      |
                                                          +--+   +--+
                                                             |   |  +-------SEQinconnue
                                                             |   |
                                                             |   |               +-Ecoli
                                                             |   |               |
                                                             |   |      +--------+salmonallaT
                                                             |   |      |        |
                                                             |   |      |        +-Kpneumoniae
                                                             +---+      |
                                                                 |  +---+             +---synechocystis
                                                                 |  |   |           +-+
                                                                 |  |   |           | +---Maeruginosa
                                                                 |  |   |           |
                                                                 |  |   +-----------+ +-----Npunctiforme
                                                                 |  |               | |
                                                                 |  |               +-+
                                                                 +--+                 |        +------------Pmarinus
                                                                    |                 +--------+
                                                                    |                          +----------synechococcus
                                                                    |
                                                                    |   +--------polaromonas
                                                                    | +-+
                                                                    +-+ +---------------Xfastidiosa
                                                                      |
                                                                      +-------Cburnetii

Bonsoir,

Je pense que ce que vous expliquez dans votre mail est une bonne analyse de la situation. C'est à dire que vous suspectez que la séquence mais vos analyses montrent une histoire différente. La phylogénie moléculaire, comme toute discipline en biologie, a ses limites, limites qui dépendent de plusieurs facteurs (type de marqueur utilisé, méthodes de reconstruction employées, vitesses d'évolution, échantillonnage taxonomique, qualité des alignements...).

Il est possible que même en soignant vos analyses, vous n'arriviez pas à mettre en évidence une origine mitochondriale. Le meilleur conseil que je puisse vous donner est reporter dans la case analyse phylogénétique, l'analyse de la situation que vous faites dans ce mail.

Une autre chose serait d'enrichir un peu votre jeu de données en séquences d'alpha-proteo, d'enlever les archaea et surtout de bien prendre des représentants variés au sein des groupes bactériens que vous utilisés (par exemple inutile de prendre E coli et les salmonelles qui sont très proches !).

Bon courage pour la fin

Céline Brochier

Merci pour votre réponse !