The chloroplast genome of Arthropodium bifurcatum : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Biological Sciences, Massey University, Palmerston North, New Zealand
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Date
2010
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Massey University
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Abstract
This thesis describes the application of high throughput (Illumina) short read sequencing and
analyses to obtain the chloroplast genome sequence of Arthropodium bifurcatum and chloroplast
genome markers for future testing of hypotheses that explain geographic distributions of
Rengarenga – the name Maori give to species of Arthropodium in New Zealand.
It has been proposed that A.cirratum was translocated from regions in the north of New Zealand
to zones further south due to its value as a food crop. In order to develop markers to test this
hypothesis, the chloroplast genome of the closely related A.bifurcatum was sequenced and
annotated. A range of tools were used to handle the large quantities of data produced by the
Illumina GAIIx. Programs included the de novo assembler Velvet, alignment tools BWA and Bowtie,
the viewer Tablet and the quality control program SolexaQA.
The A.bifurcatum genome was then used as a reference to align long range PCR products
amplified from multiple accessions of A.cirratum and A.bifurcatum sampled from a range of
geographic locations. From this alignment variable SNP markers were identified.
Putative gene annotations for A.bifurcatum were compared to published chloroplast genomes
from the Magnoliids and Monocot clades. Interesting similarities and differences have been
detected and these have been discussed.
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Keywords
Arthropodium bifurcatum, Rengarenga, Rock lily, Lilies, Native plants, Endemic plants, Edible plants, Maori, Ethnobotany, New Zealand, Genome, Genetics