Construction of a HAPPY map for the pea aphid Acyrthosiphon pisum

During the last decade our understanding of the functioning of many living organisms has been greatly facilitated by the availability of their genome sequences (all nucleotides in their DNA/heredity material). Thus we now have genome sequences for certain mammals (including humans), birds, fish, insects, plants and many micro-organisms. For insects the first full genome sequence was for the fruit fly, a highly studied model species, and the sequence, in a very user-friendly web-based database 'Fly Base', is available to the whole research community allowing many diverse uses. Since then many other insect genomes have become available allowing comparative studies of how insects have diversified and evolved. There is now a project underway to sequence the genome of a greenfly or aphid and this will extend studies to an insect species with a very different life-history (no pupal stage) and with very interesting behaviours. In an ideal world, sequencing would produce the complete genetic 'text' of the organism, spanning each chromosome from end to end without gaps. In reality, this is never possible. Even the most comprehensive sequencing projects produce a sequence which is fragmentary, like a collection of unbound (and un-numbered) pages of text. Just as the pages of a book must be ordered and bound to be of greatest use, it is important to work out the correct order of these sequence fragments (known as 'contigs') in the genome. Once this is done, it becomes much easier to analyse the genome sequence, fill in any missing pieces of sequence, evaluate its content, and search for particular features. Working out the order of the sequence contigs requires a genome map. Such a map works rather like the index of a book: it tells one where certain key words (or certain fragments of the genetic sequence) lie within the book as a whole. There are many ways to make genome maps, but one of the most versatile and accurate approaches is known as HAPPY mapping. This proposal seeks to build a HAPPY map and, in conjunction with other projects going on around the world, to eventually produce an 'AphidBase' of data for the research community. Although the genome sequence currently underway will be from one particular aphid species it is anticipated that the information obtained will be very relevant to other aphids including many which are important pests of agricultural crops, causing both direct feeding damage and transmitting plant virus diseases. Thus it will provide important information on how aphids develop resistance to insecticides, how new pesticides could be designed and potential new control strategies that don't require chemical treatments.

During the last decade our understanding of many living organisms has been greatly facilitated by genome sequencing projects. For insects the first full length sequence was for Drosophila melanogaster and since then the sequences of many other insect genomes have become available, allowing comparative studies of how insects have diversified and evolved. There is now a project underway to sequence the 525Mb genome of the pea aphid, Acyrthosiphon pisum, and it is anticipated that this will contribute greatly to studies of bacterial endosymbiosis, insect-vectored virus transmission, phenotypic plasticity and adaptation to host plants. Whilst shotgun sequence will be of immense utility to the world community of entomologists, its value can be multiplied several times over by mapping the genome to provide positional context for the contigs. This requires a physical 'map' of the genome. One suitable map would be a HAPPY map, a simple method for ordering markers on chromosomes and determining the distance between them. HAPPY mapping is based on the analysis of approximately HAPloid DNA samples using the PolYmerase chain reaction. This proposal seeks to build such a HAPPY map which will also enable the completeness and accuracy of the shotgun data to be assessed, and will provide the only viable route for local or genome-wide sequencing finishing at a later date. It will also provide a resource for comparative mapping of related aphid species to investigate genomic synteny. It is anticipated that the information obtained from the A. pisum genome will be very relevant to other aphid species including many which are important pests of agricultural crops and vectors of plant viruses. Thus it will provide important information on how aphids evolve resistance to insecticides, how to identify potential new pesticide targets and which proteins involved in host recognition might be blocked and thus provide non-chemical alternative control strategies.