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Dissecting the Genetic Basis of a Plant-Piercing Ovipositor in an Herbivorous Fly

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Dissecting the Genetic Basis of a Plant-Piercing Ovipositor in an Herbivorous Fly CUTTING EDGE INNOVATION: DISSECTING THE GENETIC BASIS OF A PLANT-PIERCING OVIPOSITOR IN AN HERBIVOROUS FLY Item Type text; Electronic Thesis Authors RAY, JULIANNE FLORENCE Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 01/10/2021 16:39:33 Item License http://rightsstatements.org/vocab/InC/1.0/ Link to Item http://hdl.handle.net/10150/613574 CUTTING EDGE INNOVATION: DISSECTING THE GENETIC BASIS OF A PLANT-PIERCING OVIPOSITOR IN AN HERBIVOROUS FLY By JULIANNE FLORENCE RAY ____________________ A Thesis Submitted to The Honors College In Partial Fulfillment of the Bachelors Degree With Honors In Molecular and Cellular Biology THE UNIVERSITY OF ARIZONA M A Y 2 0 1 6 Approved By: ____________________________________ Dr. Noah K. Whiteman Department of Ecology and Evolutionary Biology Department of Integrative Biology University of California at Berkeley OVIPOSITOR GENETICS IN SCAPTOMYZA FLAVA | 1 Abstract The evolution of herbivory within an insect lineage is often enabled by novel morphological innovations. The ancestor of Scaptomyza flava developed a serrated ovipositor nearly six million years ago, associated with an evolutionary transition to herbivory, that allows these flies to cut into mustard plants deposit eggs into the wound. We aim to identify candidate genes associated with ovipositor peg development in S. flava using a genome-wide association study (GWAS). GWAS methods are only appropriate for heritable, variable traits. Dissection and photographic profiling of ovipositors from over 700 female flies revealed variation in the number of serrated pegs within natural populations. Mother-daughter profiling showed this variation was heritable (h2 = 46%). Peg number variation among individuals followed a normal distribution, suggesting multiple genes likely influence this trait. Sequencing genomes of pools of individuals with the most and fewest ovipositor pegs from two populations identified four candidate loci affecting ovipositor peg number in S. flava. Many of these loci contribute to neural development in Drosophila melanogaster, consistent with the hypothesis that ovipositor pegs are hardened, innervated bristles. Overall, this project sets the stage for understanding the genetic and developmental basis of a key evolutionary innovation – a leaf-cutting ovipositor – in herbivorous insects. OVIPOSITOR GENETICS IN SCAPTOMYZA FLAVA | 2 Introduction Half of all insects, the most diverse class in the animal kingdom, are herbivorous. Insects with herbivorous feeding patterns face the challenge of successfully attaching eggs to or near food sources suitable for the emerging offspring: living plants. Solutions between species vary, but one common solution is the evolution of an ovipositor capable of cutting into living plant material and placing an egg within the plant (Aluja and Norrbom 2000). The fruit fly Scaptomyza flava is a promising model organism for identifying genes involved in the evolution of cutting ovipositor. S. flava diverged from common ancestors within the genus Drosophila (Drosophilidae) to become one of the few herbivorous fruit flies between six and sixteen million years before present (Whiteman et al. 2012). A key innovation linked to this drastic change in feeding behavior, the chitinous ovipositor structure used to lay eggs, is critical to parental and offspring survival and is a defining morphological feature of this species (Seraj 1994). Female S. flava utilize sharp pegs along their egg-laying ovipositor to cut into leaves and eat the contents of the damaged area before laying an egg within the cut (Figure 1). The sharp, hardened, cutting ovipositor of S. flava is an example of an evolutionary innovation enabling the evolution of herbivory. Over two years, this project addressed several questions: (1) Is the number of pegs on an ovipositor variable within and between populations? (2) Is the number of pegs on an ovipositor heritable? (3) What genes are associated with morphological variation in the peg-covered ovipositor of S. flava? OVIPOSITOR GENETICS IN SCAPTOMYZA FLAVA | 3 As pegs are thought to be modified sensory bristles (Aluja and Norrbom 2000, Atallah et al. 2014, McKay and Lyman 2005), we predicted that genes involved in neural cell development would be associated with peg number variation along the ovipositor. The results of this project could be relevant to future genetic study of a related species, Drosophila suzukii. This destructive fly devastates grape and other fruit crops worldwide by cutting into tough-skinned fruit with a sharp ovipositor and laying eggs beneath the skin inside the bored wound (Walsh et al. 2011). The cuts induce rot in the fruit before larvae emerge, rearing bacterial colonies for larvae to consume and ruining crops with a similar tool to the more-bristled ovipositor of S. flava. A deeper understanding of genes that contribute to the cutting ovipositor of S. flava could contribute to future genomic studies of this widespread fruit pest. Methods Phenotypic variation in morphology S. flava populations were founded by Andrew Gloss in July 2014 from approximately 75 (NH1 colony) and 58 (NH2 colony) wild-collected larvae near Dover, New Hampshire. Flies used in phenotypic profiling were second generation, lab-reared offspring of the wild-collected flies. Excisions of ovipositors from more than 1000 female flies were performed using a Zeiss Stemi 2000C scope and dissection lighting. Ovipositors were mounted by placing the ovipositor with ventral pegs facing away from the slide towards the coverslip OVIPOSITOR GENETICS IN SCAPTOMYZA FLAVA | 4 on 900 uL of Permount spread over two square centimeters of the slide. The coverslip was slowly brought down on the glued area and the ovipositor's position was monitored through the Zeiss scope at 50x. Each slip was allowed to dry for at least one day before measurements were taken. Individuals used for dissection were carefully individually preserved in 96-well plates in 100% ethanol at -20o C. Measurements of excised and carefully mounted ovipositor photographs taken on a Canon EOS Rebel T3i mounted on the Zeiss Stemi 2000 were completed using the program ImageJ for ovipositor serration cord length and a 1000 uM scale bar for scale calibration. Wing cord length was measured with ImageJ from the base of the musculature to the wing apex following the third longitudinal vein. Pegs were counted along the ventral edge of the ovipositor from the smallest peg at the anterior to the longest peg at the posterior apex in their linear position along the ovipositor. Along the dorsal edge of the ovipositor, peg number varied by only one peg in all specimens studied, so these pegs were not included in analysis. Peg counts and length measurements were performed manually twice for each specimen and averaged to reduce measurement error. Heritability More than 50 single-pair matings of one male and one virgin female fly from the combined NH1 and NH2 colonies were conducted on single Turritis glabara plants in Magenta boxes (Sigma-Aldrich). Each box was provisioned with cotton balls soaked in 10% honey solution to improve survivorship. For 30 matings that yielded daughters, ovipositor length and peg count was profiled (as described earlier) for every mother and OVIPOSITOR GENETICS IN SCAPTOMYZA FLAVA | 5 at least one of her daughters. Narrow-sense heritability of ovipositor peg number was calculated by regressing the phenotype of each mother against the average phenotype of her daughters. Narrow-sense heritability estimates for each trait were calculated by doubling the slope of each regression, since ovipositor traits could be measured only in mothers and not fathers. Heritability was estimated for ovipositor length, which we aimed to eliminate as a confounding variable in our search for genes underlying peg number variation. DNA extraction and genome sequencing Pools of individuals for sequencing were formed by regressing peg number against ovipositor length and selecting individuals with extreme residual peg number values for sequencing . The top and bottom 20% extreme residual flies were pooled separately. This created density-corrected pools: ovipositor peg number differed between pools, but ovipositor size did not. DNA extractions were performed with the user-developed protocol DY11 for use with the Qiagen DNeasy® Blood & Tissue Kit and TissueLyser using the thoraxes of extreme individuals separated into smaller pools that were later combined into the "high" and "low" sets for each population. Two separate populations were sequenced to approximately 40x coverage using these pools on an Illumina HiSeq 2500. Genome mapping OVIPOSITOR GENETICS IN SCAPTOMYZA FLAVA | 6 Best practices were performed for pooled sequencing analysis recommended by Schlotterer et al. (2014). Low quality reads were removed, and low quality regions were trimmed, using Trimmomatic (Bolger et al. 2014). Reads were mapped to the S. flava genome using bwa (Li and Durbin 2009). Duplicates were removed using Picard (http://picard.sourceforge.net/). Allele frequency differences among the pools with high and low peg number were tested for using the Cochran-Mantel-Haenszel test in Popoolation2 (Kofler et al. 2011). P values were Bonferroni-corrected to control the type I
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