Does the genome make sense without knowledge of the ovum?

Question

Much of the literature for laypeople seems to consider (and to spreadthe idea) that an animal (or a plant, I guess) is characterised by itsgenome. I do not know whether the same goes for more professionalliterature. Even on this site, the tag [tag:genomes] is defined as *Theentirety of an organism's hereditary information*, which seems to implythat it contains a description of all that can be be inherited.It seems to me that attempting to define an animal with the soleknowledge of its genome (let alone recreate it as envisioned by some people) does notreally make sense, without the complementary knowledge of the cellstructure of the ovum that has to interpret this genome.This question seems never to be seriously addressed in lay literature.Is it the case that this decoding machinery evolves much less than thegenome itself? This could be expected, since changing the decoder hasusually more important, global and drastic effects than changing thegenome, which may result in a very localized effect. Hence, changes tothis machinery are less likely to give a viable being.To refine that question (unless the moderator prefers this to be aseparate question):Is there any study of the diachronic evolution of that genome decoding machinery in agiven species, or of the synchronic differences between species, whichwould probably give a measure of the speed of diachronic evolution ofthat machinery?When two close species cannot mate, is it analysed (for some cases) whether it is dueto difficulties in combining the two genomes, or to the fact that theovum of one cannot properly interpret the genome of the other?

Answer 1

Hi there,

If I am understanding your question correctly, you're making the point that defining species or organisms on the basis of their genomes (i.e., DNA) alone is insufficient because for the organism to grow and develop, there has to be *stuff* inside the ovum that is able to follow the blueprint of the genome.

You're absolutely right that there is a lot inside the egg cell itself that is indispensable for development of an embryo (tons of protein, non-coding RNAs, lots of signaling molecules, energy stores, etc.). Furthermore, while some of these elements do indeed directly act to cause the transcription and translation of specific genes from the genome, they would not usually be described to "interpret" the genome.

However, all of these components of the egg cell were also produced through some pathway or another dictated by the genome. It is for this reason that in both lay and professional literature, we make the case that the genome is sufficient to define a species or organism. Everything that makes up and executes the biological "plan" for every one of its cells is written into the sequence and structure of its genome in some form or another. As a result, even the specific elements of the egg which the question refers to that "decode" the genome are also under the control of the genes that make up their pathways of action. As a result, changes to these elements also occur as a result of changes to the genetic material responsible for producing them.

Speciation generally refers to the process by which two lineages of organisms diverge so as to be unable to produce both viable and fertile offspring with each other. As a result, when we study the evolution of species, we first look for barriers preventing reproduction. These can be either pre-zygotic (occurring before the joining of the egg and sperm) or post-zygotic (occurring after the joining of the egg and sperm). An example of a pre-zygotic barrier could be different coloration in plumage that makes one species unattractive to another, or even a mountain range separating two populations, thus preventing any cross-mating from occurring in the first place. I believe that post-zygotic barriers better encompass the case the question describes, in which the genetic material from the egg and the sperm are incompatible once merged with one another, preventing the formation of a viable offspring. Generally, pre-zygotic barriers form first between populations and subsequently allow for the formation of post-zygotic barriers. However, it's oftentimes not just useful, but also essential, to consider both types of barriers to reproduction when thinking about species and the speed at which they form.

I hope that helped! :)

Answer 2

These are two very interesting questions. The first one, which I'll interpret as, "Is the genome the entirety of the information to make an individual," has a few answers. Firstly, there is non-genomic information that is occasionally hereditary: epigenetic markers (turning up or down genes with chemical modifications to the outside of the DNA); mitochondrial DNA inherited specifically by the female or egg-carrying parent (see the field of forensic anthropology); and increasingly some scientists believe that the inheritance or passing of gut/internal microbes may influence development. I encourage you to take a look at the emerging field of "Evo/Devo," or evolutionary developmental biology, which analyzes why fish and human embryos (to pick an example) look so much alike at first, but diverge over developmental time. Another example is that of identical twins: though they share "exact matches" of the coded genome, environmental regulation of how that genome gets expressed causes changes in the end product. So the answer is that genomic DNA carries enough information to make A member of your species, but not THE specific member you are hoping for (cloning, life extenstion, etc.).

An experiment was done by Craig Venter that took the entire genome of one (prokaryotic) microbe and put it in the hollowed out shell of another microbe of a different species. Over time the new microbe developed into the original species and had "normal" offspring. The toolkit for genome reading was, if not universal, similar enough to get a member of the correct species up and running, with minimal changes. (This would not work in a eukaryote without swapping mitochondial DNA as well).

For the "will it blend" question, it's often an answer of how well the chromosomes line up (during meiosis 1). Changes in oddness/evenness of chromosome number will prohibit inter-species breeding, but not always in plants ("allopolyploidy" in stawberries where chromosomes are copied twice to make new species, sometimes by inappropriate mixing). In general, plants do better at mixing/grafting/improvising than animals-- maybe their design is less fragile overall. If there are mostly just changes in the *type* of trait (lions and tigers are mostly changes to a similar template) but not the presence of *new* traits (fish have gills, dolphins have lungs), mixing can happen. Again, DNA breakage or wrong transfer during crossover is the primary indicator of offspring failure. The ovum does not count the number of chromosomes, but rather their symmetry after information exchange.

Hope this helps, and happy researching!

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tl;dr the genome is not considered the whole organism in the literature, but rather most of the organism, though that change is coming about slowly as new information is discovered.