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

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.