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  • Why not sequencing female individual in reference genome?

    Why not sequencing female individual in reference genome?
    ->
    Why not sequencing male individual in reference genome?

    Hi, I'm wondering about the sex chromosome information in public reference genome.

    If I can sequencing this species, just select the female individuals at once.

    But, In ENSEMBL (except for model orgranism, like human, mouse have the Y chr information) don't have the Y chr information in case of cow, dog...etc

    Why?
    Is it rely on my mind? or Are there the important reason?

    sorry for my ENG.
    Thanks.
    Last edited by Hyunmin; 01-02-2013, 06:12 PM. Reason: Topic Name Mistake

  • #2
    Why not sequencing female individual in reference genome?

    Hi Hyunmin,

    Hope I can partially some of your queries.

    When you speak of genome, then automatically both the maternal + paternal copies of genes (alleles) are sequenced, are not they ? Moreover, just curious to ponder- what differences the man and woman genomes would have different ?

    Just thinking, if they sequenced woman [22 Autosomes + XX], they would miss out on the Y chromosome information in a man [22 Autosomes +XY] ! Also, if they sequenced "many gametes [in terms of ovules or sperms- which are haploid (n); in that case they have chances to get specific X and / or Y populations. But then, epigenomics [methylation] wise this adventure might be more worth than for genome sequencing ! Even this is an interesting classical work: http://www.nature.com/ng/journal/v43...ll/ng.862.html

    Also, specific approaches by "Chromosome Sorting" would allow sorting and sequencing of X and or Y chromosomes from gametes for specific purposes. For example- http://www.pnas.org/content/108/1/12.long & http://www.ncbi.nlm.nih.gov/pubmed/21169219.

    I understand, even cow, dog, cats [= mammals] DO have XY chromosome mechanism (remember the Sry , SOX9 stories in text books?), but may be have not been made available by the websites you have referred!

    In plants, it is more complicated and I can direct you to some master-piece papers shedding light on sex-determination aspects in plants/ animals-



    1. http://www.amjbot.org/content/94/2/141.abstract
    2. http://www.ncbi.nlm.nih.gov/pubmed/21526970
    3. http://www.annualreviews.org/doi/abs...-042110-103914
    4. http://www.plosbiology.org/article/i...l.pbio.1001312
    5. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779942/

    Even the Wiki page on "Sex determination" was useful to me: http://en.wikipedia.org/wiki/Sex-determination_system

    Though not sure, how the "stagnant" genome is more useful than the far more "dynamic" transcriptome is more relevant for your line of thoughts or your areas of interest, esp. given the lower information/ usefulness content from the (esp with recent questions and controversies associated with the ENCODE Project: http://www.nature.com/encode/#/threads) & http://www.nature.com/nature/journal...l/489052a.html. I mean, if a subtle mutation at SRY can reverse/ influence sexuality or temperature can regulate sex-determination in reptilia, then how and why the Sex chromosome information would matter much ? And if I recall, in interesting Platypus (genome?) sex regulation is a results of interplay of only "the number of X" and no questions of "Y"s there. Even in nature, it is always thought that Y is an "abberation/ exception" in the world of "X"s.

    Hope, I have answered some of your curiosities, if not all and direct/ relevant issues.

    Thanks and best wishes,

    Biswa

    Originally posted by Hyunmin View Post
    Why not sequencing female individual in reference genome?
    ->
    Why not sequencing male individual in reference genome?

    Hi, I'm wondering about the sex chromosome information in public reference genome.

    If I can sequencing this species, just select the female individuals at once.

    But, In ENSEMBL (except for model orgranism, like human, mouse have the Y chr information) don't have the Y chr information in case of cow, dog...etc

    Why?
    Is it rely on my mind? or Are there the important reason?

    sorry for my ENG.
    Thanks.

    Comment


    • #3
      Originally posted by Biswapriya View Post
      Just thinking, if they sequenced woman [22 Autosomes + XX], they would miss out on the Y chromosome information in a man [22 Autosomes +XY] ! Also, if they sequenced "many gametes [in terms of ovules or sperms- which are haploid (n); in that case they have chances to get specific X and / or Y populations.
      Thank you for your kindly reply.
      It's very helpful for me.

      In fact, I wrote them incorrectly.
      My real question is "Why not sequenced male individual in ENSEMBL mammal reference genome?"

      I agreed with your opinion. sequenced male individual is more helpful than female indiviudal aspect of that we can get the Y chromosome information. so, I wonder why not apply the male individual in case of cow, dog..etc

      Best wishes,
      Hyunmin

      Comment


      • #4
        One of the reasons for sequencing females is that since there are two copies of the X-chromosome (i.e. same as the autosomes) you can get a higher sequencing coverage for the X than when sequencing males. With males your sexual chromosome sequencing coverage ends up being only half of that for autosomes, making an assembly of similar quality more difficult and expensive.

        Comment


        • #5
          Official "reference" genomes for model organisms are not necessarily from one, single individual. I believe the human reference has different portions of it derived from three different individuals. There would be no issue with using sequence from a female for the bulk of the reference and adding male specific sequence (e.g. chrY) from a male. Remember, genome assemblies should not be taken as the absolute true and accurate genome of any individual organism. They are merely computaionally convenient approximations of biology.

          Comment


          • #6
            Originally posted by kmcarr View Post
            computationally convenient approximations of biology
            I really like that phrase and intend to use it often. Thanks.

            Comment


            • #7
              Originally posted by Joann View Post
              Originally Posted by kmcarr
              computationally convenient approximations of biology
              I really like that phrase and intend to use it often. Thanks.
              I just want to make clear I am paraphrasing others with that quote. (I'm hardly that pithy when left to my own devices.) Notably Titus Brown's review of the Assemblathon 2 paper. There was a thread on SeqAnswers recently which also linked to Titus' review and I believe had a more eloquent quote than mine but I'll be damned if I can find it now.

              Comment


              • #8
                Originally posted by kmcarr View Post
                Official "reference" genomes for model organisms are not necessarily from one, single individual. I believe the human reference has different portions of it derived from three different individuals.
                Of topic, but I thought the number was in the 20s or even higher, but most of it was actually just 1 person.

                Comment


                • #9
                  Because sequencing the X chromosome in a male is going to be much harder than in a female (with two copies of each sequence).

                  The assembler programs for de-novo assembly have to make assumptions about coverage to separate the multi copy sequences from the single copy sequences. If you have a single X chromosome in the (male for mammals) individual you sequence, the depth of coverage of a contig or scaffold would be half that observed for autosomal contigs. Because until the genome is finished, we do not know which chromosome a contig goes to, and therefore from a male many of the X or Y chromosome contigs would be flagged for low coverage and discarded or ignored as likely errors, or highly diverged sequences where both copies of a sequence can not be paired on autosomes.

                  With limited sequencing input, on de-novo assembly it comes to a choice of either a poorly assembled X and Y chromosome or a much better assembled X chromosome only. Many genome projects choose for the better assembled X chromosome.

                  Comment

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