May 5, 2012

Primer development for the plastid region ycf1 in Annonaceae and other magnoliids

This article identifies the usability of ycf1 using primers to identify the plasid gene within the magnoliid taxa. This hypothetical chloroplast open reading frame 1, more commonly identified as ycf1, codes a region of 5,500 base pairs, and is virtually present in many plastid genomes. It is typically used in analyzing orchids and Pinus, making the use of it in magnoliids unique and somewhat rarely studied. Using an array of species across many families, the samples were able to specifically identify the usage of ycf1. An array of primers were used to amplify various portions, to amplify various nucleotide regions. By sequencing roughly 2000 base pairs within ycf1 in over 20 individuals, the researchers were able to examine the phylogenetic utility relative to other plastid regions. The genera Deeringothamnusand Asimina (Annonaceae) was used due to its close proximity. Through various PCR deviations using different primers revealed the discrepancy of ycf1 among species, discovering the higher number of informative characters. Finally, the resulting factors proved that ycf1 proves to be easily amplified and sequenced vastly more than other common markers such as matK and trnL-F. The study indicates that ycf1 has great potential utility.

References:

Neubig, K., & Abbott, J. (2010). Primer development for the plastid region ycf1 in annonaceae and other magnoliids. American Journal of Botany, Retrieved from http://www.amjbot.org/content/97/6/e52.full

Posted in Literature, ycf1
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April 6, 2012

ycf1 from 4-1 to 4-11

Carly S., Mary C., and Tram N. performed the PCR amplification of DNA’s 4-1 through 4-11 for the targeting region of ycf1. The purpose of this experiment was to amplify using PCR ycf1 from orchid species DNAs 4-1 through 4-11, which were previously extracted. The last lane on the far right in the second row (lane M) served as our marker lane. The products were then collected to run the Agarose Gel Electrophoresis. A total of twelve lanes were loaded as described in figure 1.

Figure 1: Agarose gel electrophoresis of ycf1 gene 4-1 to 4-11. Lane 1: H2O (control). Lane 2-12: ycf1 4-1 to 4-11. Lane M: protein markers

As evident by figure 1, the experiment was sucessful since most of the samples produced either strong (++) or mild (+) success rate, except for 10-y, (lane 11, Cleisostoma subulatum), also shown by table 1. The error could have occurred in several occasions. One sight of possible error was during the loading of the sample into the lanes during the gel electrophoresis. This procedure was obscured when the samples were loaded into the lanes improperly, being loaded while on the bench and not in the proper location. The samples were loaded into the gel wells without being submerged in running buffer in the gel electrophoresis apparatus. However, only one sample was unsuccessful, thus we can assume this error didn’t have an extreme effect on the samples. The relative size of the amplified product was larger than a thousand base pairs.

Table 1: PCR results of ycf1 4-1 to 4-11. The species names were described. (++) denotes a strong amplificaion, (+) denotes an amplification , and (-) denotes a weak ampflication.

This post was an equal collaborative effort of Carly and Tram.

Posted in ycf1
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March 2, 2012

Holcoglossum flavescens

The specimen used in lab for the DNA Extraction. Photo by Carly Smith

The specimen used in lab for DNA Extraction. Photo by Carly Smith

Holcoglossum flavescens Schlechter is a winter blooming plant that is a member in the tribe Vandeae. It belongs to the subtribe Aeridinae. This plant is frequently found in China, specifically within the Forrest of Yunnan.

This epiphytic plantis also found in rain forest growing on another plant. Holcoglossum flavescens blooms with flowers opening with white and tints of yellow in the winter, and opens to approximately 2.5 cm wide. Its leaves are roughly 5-6 cm long. This plant typically requires full sunlight along with cool transitional temperatures and frequent watering.