0
$\begingroup$

I'm writing a grant proposal, and part of the research will involve sequencing and comparing DNA from trees in America and Japan. How does one analyze the genome of a tree and compare it to a conspecific?

$\endgroup$

closed as too broad by canadianer, Remi.b, kmm, David, AliceD Oct 26 '17 at 21:10

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. Avoid asking multiple distinct questions at once. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

  • 1
    $\begingroup$ how is that different from sequencing animal genome? $\endgroup$ – aaaaaa Oct 22 '17 at 23:14
  • $\begingroup$ I don’t know. Is it different? $\endgroup$ – Ian Oct 23 '17 at 1:45
  • 1
    $\begingroup$ Are you trying to sequence the entire genome or just portions of it? This review paper may help you get started, specifically the portion titled "how do we sequence" ncbi.nlm.nih.gov/pmc/articles/PMC1456863 $\endgroup$ – John Oct 23 '17 at 4:13
  • 1
    $\begingroup$ it seems like you haven't done studying on your own, which is the first step usually. Genome sequencing is pretty common these days, and a lot of information is available. Maybe start with simple googling "how to sequence genome". Also, as grant writing goes, if you include work that you don't know how to do maybe you should seek collaboration with genomics people $\endgroup$ – aaaaaa Oct 23 '17 at 10:15
  • 1
    $\begingroup$ I agree with aaaaaa - if for a grant, the level of this question indicates you need to do way more reading of the literature than you apparently have been. (Otherwise you're just wasting the grant committee's time.) For example, a quick search finds a list of sequenced plant genomes - you can start from the references there to see how they did it. -- That said, you're probably looking for "genotyping" rather than "whole genome sequencing". Doing a web search for "genotyping trees" pops up a number of papers you can start from. $\endgroup$ – R.M. Oct 23 '17 at 18:55
1
$\begingroup$

In journal articles, they are doing many studies every year describing the state of the art tools and procedures for sequencing plant genomes.

by researching 5 minutes you have results of this kind:

http://www.pnas.org/content/95/16/9693.full

Protocols involved commercially available kits (e.g., Qiagen’s RNeasy Plant Minikit), non-commercial RNA extraction lab protocols (e.g., CTAB, acid phenol) and hybrid methods that combined components of both commercial kits and lab protocols. The detailed protocols used for all isolations are available online in Appendix S1. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050226

Tissue and organ samples for Northern blot analysis of gene expression patterns were taken during the growing season and frozen in liquid nitrogen, then stored at −80°C. Shoot-tip samples are the terminal 1–2 cm of succulent stem tissue from elongating branches and terminal leaders. Immature xylem was harvested with a vegetable peeler from the surface of woody stems after removal of the bark, and includes cells with primary cell walls derived from the cambial zone through the zone of radial cell expansion. Compression wood and side wood immature xylem RNAs were those used for preparation of the libraries, whereas vertical immature xylem denotes samples taken from stems of control trees growing vertically. The tissue described as “phloem” was collected from the inner surface of the bark of vertical stems and actually includes periderm and other tissues as well as active phloem. Planings were collected from the surface of vertical woody stems with a wood plane after immature xylem was harvested and includes cells that have formed secondary cell walls strong enough to resist harvesting by the vegetable peeler. Needle samples were partially expanded juvenile needles.

here are some more texts for you to check

http://www.pnas.org/content/106/31/12794.full

https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214

From_field_to_film_Rapid_sequencing_methods_for_field-collected_plant_species

It took me 5 minutes to find these informations by searching articles for

plant sequencing methods

$\endgroup$

Not the answer you're looking for? Browse other questions tagged or ask your own question.