Using comparative genomics to uncover the origins of phenotypic modularity in squamate reptiles

Project Information

ULTRAMOD

Grant agreement ID: 101027832

DOI

10.3030/101027832

Project closed

EC signature date 15 April 2021

Start date 1 July 2021

End date 30 June 2023

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 212 933,76

EU contribution

€ 212 933,76

Coordinated by

NATURAL HISTORY MUSEUM
United Kingdom

Periodic Reporting for period 1 - ULTRAMOD (Using comparative genomics to uncover the origins of phenotypic modularity in squamate reptiles)

Reporting period: 2021-07-01 to 2023-06-30

Summary of the context and overall objectives of the project

What is the problem/issue being addressed?
A whole genome is a complete sequence of the DNA that each cell in a living organism contains. With the undertaking of the human genome project, we entered a new era of studying DNA where we can obtain complete sequences of chromosomes; the building blocks of genomes. Over evolutionary time, chromosomes diverge in their organization and content as species evolve and diversify. Understanding exactly how these changes occurred is a major goal in biology. Since the human genome project, DNA sequencing technology has evolved vastly substantially increasing the number of genomes across different species., yet with more genomes comes greater analytical challenges. Despite constant methodological advances in genomics, it is still difficult and time consuming to compare the genome structure of different species and identify how physical characteristics of organisms are influenced by changes in chromosome structure.
During this project, we focussed on specific genomic sequences that are highly conserved in vertebrate animals. These ~2000 bits of vertebrate genomes have remained the same despite 300+ million years of evolution. They are called ‘Ultraconserved Elements’ or UCEs. Each UCE has a different nucleotide sequence, yet individual UCEs are near identical across more than 33,000 species of tetrapods (a group that contains birds, reptiles, amphibians, and mammals). Scientists are not completely sure why UCEs have remained so conserved over evolutionary time, but prominent hypotheses include that they are important for developmental regulation and/or the stability of genome structure. In the ULTRAMOD project, we leverage the conserved nature of UCEs to compare different chromosomes across species with the goal of yielding new insights into how chromosome structure differs across species.

Why is it important for society?
Genomic data are imperative to human society, from tracking strains of disease-causing organisms to identifying how prone someone is to a particular condition, understanding underlying drivers of evolutionary change, adaptation and more. Genome data are also used to cultivate and breed plants and animals as well as make them more resistant to disease and environmental stress. The ability to compare and analyse whole genome data is limited by computational resources. Methods such as ours that do not require access to high performance computing will play a key role in making genomics more accessible to everyone, notwithstanding political borders and power differences.

What are the overall objectives?
Based on the availability of genomes, we expanded the scope of ULTRAMOD, which was originally restricted to lizards and snakes, to include all tetrapod animals. We sought to answer several key questions about UCEs in different species. Initially we asked three questions. First, how are UCEs distributed across the genome? Second, do all chromosomes have UCEs? Third, how can we compare the position of UCEs on many different species at the same time? Because specific UCEs are linked to genes that play a key role in limb development, we were also interested in their link to limb loss which is observed in some tetrapod groups like snakes and lizards. To achieve these objectives, we developed a method to landmark UCEs on the chromosomes of different species and are also sequencing a high-quality genome from an endemic limbless lizard from Sri Lanka.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Before tackling our research questions, we assessed genome availability and available methods we could use. During these steps, we faced several challenges in finding the methods that would capture change across entire chromosomes, in a realistic timeframe, and also provide us a quantitative measure of chromosomal variation. Therefore, we developed a novel pipeline to achieve our main objectives. We utilised published high-quality tetrapod genomes onto which we mapped UCEs. Using the position of UCEs within every genome, we singled out all the common UCEs and used them to measure similarities and differences of chromosomes. To do this, we relied on the principles of ‘landmarks’ commonly used to measure change in morphology. Landmarks are essentially points on an object whose position might vary across species, but whose identity is the same. For example, the tip of the nose in one species compared to the tip of the nose in another species. By using common points across different organisms, one can establish differences (like the length of a nose) in a quantitative framework. We used UCEs as such common points across chromosomes to measure physical changes in chromosome structure. We implemented this method using both real and simulated chromosomes from 60+ species of tetrapod animals. Importantly, the pipeline we developed requires relatively low computational resources compared to the high-computational demand of most comparative genomic methods. We found that our method effectively captures important differences in the structure of chromosomes simultaneously for multiple species. Two project members, Ashwini V. Mohan and Jeffrey W. Streicher, have disseminated the findings from this part of the study in >5 international conferences to large audiences.
Even though we have utilised UCEs as our landmarks, we discovered that landmarks on a genome could be any conserved sequence, so our method also may be more broadly applied in genomics. We have drafted the first manuscript from this project that contains both the newly proposed method and its implementation on mammalian genomes. We will submit this work to an internationally renowned scientific journal. In addition to this work, we have initiated a study comparing measures from genomic landmarks with morphological landmarks. We have most of the data necessary and are currently filling gaps. We will also soon receive the new genome sequence of the Sri Lankan limbless lizard which will add valuable information to a clade of lizards that have lost limbs across their evolutionary history >30 times. Our goal with this genome is to further our understanding of the molecular basis of limb loss in squamates, and to uncover whether these molecular bases are common across snakes and other limbless lizards.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The ULTRAMOD pipeline has revealed evidence that the structure of conserved chromosome regions in the genome assembly of the domestic pig is different when compared to other mammals. This could be explained by real differences or also be evidence that the chromosomes of the pig were assembled incorrectly. We are currently scrutinizing this result to understand which explanation is more likely. This example reveals how our pipeline can improve the understanding of genome structure in commercially important species like the domestic pig. This may have wider socio-economic impacts by refining our understanding of a staple agricultural species.

Bridging genomics and morphometrics: landmark based estimates of genomic disparity