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Overview

Project Highlights: 3 points as a bulleted list

The project will:

  • Increase understanding of fundamental processes that drive the evolution and diversification of genome structure and function
  • Test the role of an important type of selection - sexually antagonistic selection - on the evolution of sex-biased gene expression
  • Enable the student to gain skills and experience in state-of-the-art next generation RNA sequencing methods to investigate gene expression

Females and males have almost identical genomes but are exposed to conflicting selective pressures. It is hypothesised that these conflicting selective pressures - known as sexually antagonistic selection – are the explanation for multiple independent evolutions of sex-biased gene expression and also sex chromosomes [1]. However, empirically testing the role of sexually antagonistic selection has been hampered by the lack of suitable experimental systems as sex differences are often longstanding [2]. Using a model system we have developed [3-5] – the tadpole shrimp, Triops sp. - this project will test whether changes in the mode of sexual reproduction influences the magnitude and extent of sex-biased gene expression.

We have shown that tadpole shrimps (Triops) show multiple transitions between separate sexes (dioecy) and individuals with male and female function (hermaphrodites) [3, 6]. Importantly such changes alter the strength of sexually antagonistic selection [7]. We therefore have a system where sexually antagonistic selection differs so its role on sex-biased gene expression to be tested. Furthermore, we have shown that sex is genetic in Triops cancriformis and that sex chromosome regions are larger in dioecious populations than in hermaphrodite populations, a pattern consistent with a reduction in sexually antagonistic selection [5].

This PhD will investigate two species where hermaphroditism has evolved independently and there are both dioecious and hermaphrodite populations (Triops cancriformis and Triops longicaudatus).

The student will test whether:

  • genes with female biased expression in dioecious populations are less biased in hermaphrodites
  • genes with male biased expression in dioecious populations less biased in hermaphrodites
  • There is an effect of genome position (e.g. within or outside the sex chromosome region) of genes on the degree of change in expression bias.
  • There are convergent patterns of change in Triops cancriformis and Triops longicaudatus.

Objectives:

  1. To develop sex-specific genetic markers for identification of males, females and hermaphrodites in T. cancriformis / longicaudatus.
  2. To identify genes located within the sex specific region of males, females and hermaphrodites in T. cancriformis / longicaudatus.
  3. To test for a reduction in the differential expression of sex-associated genes in the transition from dioecy to hermaphroditism in T. cancriformis / longicaudatus.
Triops cancriformis. Some populations are composed of outcrossing males and females leading to high levels of sexually antagonistic selection.  In other populations there are self -fertilising hermaphrodites leading to much reduced levels of sexually antagonistic selection.

Methodology

Triops will be reared in the laboratory until adulthood and both RNA and DNA extracted.

Sex specific markers (objective 1) will be designed by identifying sex associated genome scaffolds (available from our ongoing genome sequencing project) that are marked by known sex-specific RAD markers [3]. PCR primers will be designed and tested on adults of known sex.

Sex specific region genes (objective 2) will be identified in silico from the annotated genome in conjunction with known sex-specific RAD markers [5] 

Differential expression of genes will be measured using Illumina based RNA sequencing analysis of samples of males and females (dioecious pop.) and hermaphrodites in hermaphrodite only populations. After quality control reads will be mapped to genomes and differential expression measured using established bioinformatic methods (objective 3).

Training and Skills

CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes.

Bioinformatics skills are essential in ‘big data’ heavy modern biology, especially evolutionary and environmental biology. The successful student will gain highly transferable skills in: biological computing and programming (e.g. PERL, Python, R), handling next generation sequencing data in a Linux environment, transcriptome assembly, molecular evolutionary analysis, and manuscript preparation and giving presentations.

In addition to CENTA training the successful student will receive tailored training from a number of routes:

  • From supervisors directly
  • Via workshops offered Leicester’s Biostatistics and Bioinformatics Support Hub (BBASH)
  • From University of Leicester courses (e.g. R)
  • By taking elements of Leicester’s Bioinformatics MSc (e.g. Python)

Timeline

Year 1: Sample collection, Triops husbandry, Development of sex specific markers, RNA extraction, RNA sequencing. Bioinformatics skills development.

Year 2: Differential gene expression analysis of T.cancriformis and T.longicaudatus. Bioinformatics skills development.

Year 3: Analysis of genome position effects. Comparitive analysis of T.cancriformis and T.longicaudatus differential gene expression. Manuscript preparation / thesis preparation.

Partners and collaboration (including CASE)

Dr Africa Gomez (Hull) is an evolutionary biologist, an expert on Triops and a long-time collaborator of Dr Hammond. Gomez and Hammond successfully supervised a NERC CASE PhD student (Dr T. Mathers, 3 papers, currently postdoc at the Earlham Institute) and have collaborated on the genome sequencing of Triops cancriformis. Mallon and Hammond have recently supervised a NERC funded PhD student (Mark Harrison, currently a postdoc at University of Muenster, 1 paper, 2 in prep) that used RNAseq [8], the primary research method used in this project.

Hammond, Mallon and Gomez therefore have complimentary expertise and constitute a strong supervisory team.

Further Details

Rob Hammond, Department of Genetics, University of Leicester.

rh225@le.ac.uk

phone: 0116 252 5302