Survey of sequence polymorphisms of the internal transcribed spacer region in nematodes from the Botanic Gardens.
- Description
- Source of support
- Duration
- Project team
- Virtual nematode collection from UCRBG
- Links
Description
In the past researchers have found polymorphisms associated with the internal transcribed spacer (ITS) region in the DNA of certain plant parasitic nematodes. Within DNA are regions that are coding and which contain genes that are transcribed, while there are also regions of non-coding DNA (like the internal transcribed spacers) that theoretically do not hold any important information for transcription. Non-coding DNA generally evolves much faster and is therefore more appropriate for detecting sequence variations between and within individuals.
The purpose of this study will be to use the ITS region to screen for polymorphisms in a diverse range of nematodes. This will help me to establish a rough estimate of variation in other groups of nematodes besides plant parasites. I have chosen the Botanic Gardens as my site for collecting nematodes for a few reasons. One reason is that with the diversity of plants inhabiting the different gardens there should be an equal diversity of nematodes throughout the different areas of the gardens as well. Also there should be a wide variety of introduced species from all over the world within the different habitats because of the various plants that have been introduced. Finally, a fellow student is currently looking at the diversity of nematodes throughout the Gardens so by the onset of my project I will know which area will have the highest diversity of nematodes.
My plan is to use five individual nematodes from ten different species to obtain ITS sequence, and to check these sequences for multiple peaks indicating intragenomic polymorphism, as well as for differences between individuals of the same species. I will first collect 4 samples of 500 ml soil in an area of the Botanic Gardens where the highest nematode diversity is found. Five individuals each from ten different species will be selected from the samples, i.e. a total of 50 nematodes. All individual nematodes will be looked at using microscopy and video captured for the purpose of making morphological observations. The DNA of each individual will then be extracted and used for amplification in Polymerase Chain Reaction (PCR). After PCR I will check the size of the amplified DNA by electrophoresis and clean up the PCR products by removing leftover primers and single nucleotides. The next step will be to give the cleaned products to the Core Instrumentation Facility of the UCR Genomics Institute for sequencing. After completion of the sequencing I will align and analyze the resulting data to look for polymorphisms in the ten nematode species.
Source of support
Duration
January 3 - June 30, 2003
Project team
Links
- Website of the UCR Botanic gardens
- Website for the UCR Genomics Institute