Author Archives: dc0127

Highly variable YCF1 useful for evaluating plant phylogeny at low taxonomic levels.

Twelve genera scanned to find highly variable regions of the chloroplast genome.Twenty-three loci were selected, the most variable were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnSUGA-trnGUCC, petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnSUGA-trnGUCC, trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity. The chloroplast genome is often used to determine plant phylogeny but becomes difficult in closely related species. Finding regions with more variability allows lower level taxonomy. The ycf1 region was found to have the most variability among the regions looked at. To solve phylogenetic problems at the species level,regions with very high evolutionary rates are needed. Greater availability of such regions will increase the ability to resolve such identification problems.

Reference:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325284/?tool=pmcentrez

Wenpan Dong,1,2 Jing Liu,1,3 Jing Yu,1,3 Ling Wang,2 and Shiliang Zhou1*

Preperation of successfully amplified ycf1 from DNA’s 4-12 through 4-22

Danny Cannon and Trevor R. on March 3, 2012 use exonuclease and alkaline phosphatase to clean up samples 4-12 through 4-13.  The following chart shows that we obtained high yields on all except for 4-13, which failed.

4-12

391.21

4-14

404.72

4-15

418.95

4-16

376.62

4-17

382.14

4-18

381.99

4-19

396.18

4-20

425.07

4-21

400.08

4-22

397.63

Chroniochilus virescens

Chroniochilus virescens (Ridl) of the subtribe Aeridinae is found in hilly forest of Malaysia,Thailand, and Borneo at elevations of 500 to 1000 meters. It’s one inch, very fragrant blooms appear in the summer, one per day for a total of 8 bloom inflorescence. The rachis, a spike of flowers is strongly flattened. The leaves are short, thick and spreading in nature, extending much further than the inflorescence.

Picture by Danny Cannon

DNA extracted from this plant.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Reference:

J.B. Comber 2000. Orchids of Sumatra. Royal Botanic Gardens,Kew

http://www.orchidspecies.com/chronvirescens.htm

http://www.nationaalherbarium.nl/pubs/orchidweb/genera/Chroniochilus/Chroniochilus.htm

http://www.orchidsonline.com.au/node/10907