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?
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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:
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
It took me 5 minutes to find these informations by searching articles for
plant sequencing methods