f******p
发帖数: 178 | 1 一个单拷贝基因在二倍体中的两个copies叫什么？ alleles?
在四倍体中，是不是有两个paralogs, 每个paralog 有两个alleles？
对于多倍化发生时间较短的四倍体，难以区分各个paralog，是不是四个copies都可以
叫allele? | f******p
发帖数: 178 | 2 没人愿意帮忙吗？
【在 f******p 的大作中提到】
: 一个单拷贝基因在二倍体中的两个copies叫什么？ alleles?
: 在四倍体中，是不是有两个paralogs, 每个paralog 有两个alleles？
: 对于多倍化发生时间较短的四倍体，难以区分各个paralog，是不是四个copies都可以
: 叫allele?
| y**********n
发帖数: 478 | 3 经典遗传学的东西怎么跟现代基因学联系起来有时候确实很头大。我试着解释下，先贴
一段wiki上的：
“An allele (UK play /ˈæliːl/ or US /əˈliːl/)
is one of two or more forms of a gene or a genetic locus (generally a group
of genes).[1][2] The form "allel" is also used, an abbreviation of
allelomorph. Sometimes, different alleles can result in different observable
phenotypic traits, such as different pigmentation. However, many variations
at the genetic level result in little or no observable variation.
Most multicellular organisms have two sets of chromosomes, that is, they are
diploid. These chromosomes are referred to as homologous chromosomes.
Diploid organisms have one copy of each gene (and therefore one allele) on
each chromosome. If both alleles are the same, they are homozygotes. If the
alleles are different, they are heterozygotes.
A population or species of organisms typically includes multiple alleles at
each locus among various individuals. Allelic variation at a locus is
measurable as the number of alleles (polymorphism) present, or the
proportion of heterozygotes in the population.”
所以说不管二倍体还是四倍体只要是一个"genetic locus"都是一个allele，单基因情
况下对应SNPs。 不过经典遗传学上的“allele”是从表型上的出来的，有时候可以对
应到很多基因。所以多基因的情况下怎么对应过去我也不知道。
paralog是完全不同的概念吧，我知道进化上是指从一个祖先基因复制来的两个拷贝。
有没有其他意思不清楚
解释错了楼下指正 | l**********1
发帖数: 5204 | 4 only for paralogous
please go to
//www.ncbi.nlm.nih.gov/pubmed/15865991
its page one:
What is paralogy?
Since Darwin, for most biologists (or at least, for evolutionary biologists) homology has
come to mean something like ‘similarity due to common descent’, to distinguish it from
similarity due to convergent evolution. An accurate understanding of the relationships
between living things depends upon correctly identifying homologous characteristics of
an organism from other similarity. A classic example would be the wings of bats and
birds, which do not share a common evolutionary origin as wings. These wings and the
limbs of other terrestrial vertebrates look very different but are truly homologous.
Similarly, the genes of an organism can be homologues – genes share a common
ancestor as features of an organism, and all mammal haemoglobins are descended from
a haemoglobin gene present in the ancestor of mammals, just as mammal limbs are
descended from the limbs of this ancestor.
In genetics, however, homology can be a more complex phenomenon, because genes
can be homologous in at least two distinct ways (Fitch, 2000). As well as descending
from an ancestral species, genes also share a common ancestor as genes, in that
related genes have arisen by duplication and gradual mutation. For example, all globin
genes descend from a common ancestral globin gene. Fitch (1970) proposed new terms
for these two classes of homology among genes. If the most recent common ancestor of
two genes is a gene duplication event the genes are paralogous, otherwise they are
orthologous (see figure 1). To use Fitch’s original example, a and b haemoglobin are
paralogs, while a haemoglobin in man and mouse are orthologs.
Ps; if you had interesting to below recent reports:
please,
//www.ncbi.nlm.nih.gov/pubmed/21861918
//www.ncbi.nlm.nih.gov/pubmed/19014489
)
group
observable
variations
are
【在 y**********n 的大作中提到】
: 经典遗传学的东西怎么跟现代基因学联系起来有时候确实很头大。我试着解释下，先贴
: 一段wiki上的：
: “An allele (UK play /ˈæliːl/ or US /əˈliːl/)
: is one of two or more forms of a gene or a genetic locus (generally a group
: of genes).[1][2] The form "allel" is also used, an abbreviation of
: allelomorph. Sometimes, different alleles can result in different observable
: phenotypic traits, such as different pigmentation. However, many variations
: at the genetic level result in little or no observable variation.
: Most multicellular organisms have two sets of chromosomes, that is, they are
: diploid. These chromosomes are referred to as homologous chromosomes.
| l**********1
发帖数: 5204 | 5 just for this enquiry:
> 在四倍体中，是不是有两个paralogs, 每个paralog 有两个alleles？
一个单拷贝基因在四倍体中 how much copy or which kind of distribution that
单拷贝 or duplication 单拷贝基因?
Can you let me know the answer?
【在 f******p 的大作中提到】
: 一个单拷贝基因在二倍体中的两个copies叫什么？ alleles?
: 在四倍体中，是不是有两个paralogs, 每个paralog 有两个alleles？
: 对于多倍化发生时间较短的四倍体，难以区分各个paralog，是不是四个copies都可以
: 叫allele?
| f******p
发帖数: 178 | 6 一个常染色体上的单拷贝基因在四倍体中 通常最多有四个拷贝
同一个基因本来有两个拷贝（一个父本一个母本），在基因组整体加倍后多了两个拷贝
（一个父本的，一个母本的）
无论基因组加倍是自身加倍还是与关系很近的种杂交（可以从构建的系统树上看出来）
导致的加倍，它们在染色体上的位置应该是一样的，所以也符合allele的定义
【在 l**********1 的大作中提到】
: just for this enquiry:
: > 在四倍体中，是不是有两个paralogs, 每个paralog 有两个alleles？
: 一个单拷贝基因在四倍体中 how much copy or which kind of distribution that
: 单拷贝 or duplication 单拷贝基因?
: Can you let me know the answer?
| f******p
发帖数: 178 | 7 谢谢回复，有上面的困惑主要是看到不同的文章中不同的人用不同的词
)
group
observable
variations
are
【在 y**********n 的大作中提到】
: 经典遗传学的东西怎么跟现代基因学联系起来有时候确实很头大。我试着解释下，先贴
: 一段wiki上的：
: “An allele (UK play /ˈæliːl/ or US /əˈliːl/)
: is one of two or more forms of a gene or a genetic locus (generally a group
: of genes).[1][2] The form "allel" is also used, an abbreviation of
: allelomorph. Sometimes, different alleles can result in different observable
: phenotypic traits, such as different pigmentation. However, many variations
: at the genetic level result in little or no observable variation.
: Most multicellular organisms have two sets of chromosomes, that is, they are
: diploid. These chromosomes are referred to as homologous chromosomes.
| l**********1
发帖数: 5204 | 8 so what is relative to "paralogous" concept from your mentioned ?
【在 f******p 的大作中提到】
: 一个常染色体上的单拷贝基因在四倍体中 通常最多有四个拷贝
: 同一个基因本来有两个拷贝（一个父本一个母本），在基因组整体加倍后多了两个拷贝
: （一个父本的，一个母本的）
: 无论基因组加倍是自身加倍还是与关系很近的种杂交（可以从构建的系统树上看出来）
: 导致的加倍，它们在染色体上的位置应该是一样的，所以也符合allele的定义
| f******p
发帖数: 178 | 9 因为“Two genes are to be paralogous if they diverged after a duplication
event”
http://www.icp.ucl.ac.be/~opperd/private/orthol.html
有些文献中称四倍体中只有两个paralogs，如下面这个：
http://mbe.oxfordjournals.org/content/22/5/1193.short
If duplication of the RAG-1 gene occurred only by
genome duplication, diploids would be expected to have one copy, tetraploids
two, octoploids four, and dodecaploids
six.
对四倍体挑几十个克隆测序后，你会发现，除去PCR chimeras以后，通常（特别是异源
多倍体）你会得到两组不同序列（所谓的两个paralogs），但在每组内部也会有两小类
不同序列（父本和母本），所以另一些文章就直接说有4个alleles
如下面这篇：
http://www.sciencedirect.com/science/article/pii/S1055790310001
按照我的理解，
第一种做法忽略了paralog内部的差异。父本和母本的序列差异是客观存在的，到底选
哪个来代表这个paralog呢？没有根据。因为你也没法说出哪个就是父本，哪个就是母
本。
第二种做法忽略了两大类序列的明显不同。对于杂交形成的四倍体来说，那两大类一个
是父源的，一个是母源的。
所以我才有在主贴中的疑问。
非常感谢你的回复。
【在 l**********1 的大作中提到】
: so what is relative to "paralogous" concept from your mentioned ?
| l**********1
发帖数: 5204 | 10 经典遗传学的东西跟现代基因学无法完全一致起来 有时侯是controversial..
tetraploids
【在 f******p 的大作中提到】
: 因为“Two genes are to be paralogous if they diverged after a duplication
: event”
: http://www.icp.ucl.ac.be/~opperd/private/orthol.html
: 有些文献中称四倍体中只有两个paralogs，如下面这个：
: http://mbe.oxfordjournals.org/content/22/5/1193.short
: If duplication of the RAG-1 gene occurred only by
: genome duplication, diploids would be expected to have one copy, tetraploids
: two, octoploids four, and dodecaploids
: six.
: 对四倍体挑几十个克隆测序后，你会发现，除去PCR chimeras以后，通常（特别是异源
| f******p
发帖数: 178 | 11 这样做行不行？给个建议
四倍体
Paralog I-1
Paralog I-2
Paralog II-1
Paralog II-2
对于近期分化的四倍体，有时候没法知道哪个是I, 哪个是II，该怎么办呢？
【在 l**********1 的大作中提到】
: 经典遗传学的东西跟现代基因学无法完全一致起来 有时侯是controversial..
:
: tetraploids
| l**********1
发帖数: 5204 | 12 >对于近期分化的四倍体，有时候没法知道哪个是I, 哪个是II，该怎么办呢？
try with CryoEM 10 Å level 设法知道哪个是I, 哪个是II，
details please go to
//cryoem.berkeley.edu/cryoem
and
//mcb.berkeley.edu/index.php?option=com_mcbfaculty&name=nogalese
【在 f******p 的大作中提到】
: 这样做行不行？给个建议
: 四倍体
: Paralog I-1
: Paralog I-2
: Paralog II-1
: Paralog II-2
: 对于近期分化的四倍体，有时候没法知道哪个是I, 哪个是II，该怎么办呢？
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