Periodic Reporting for period 1 - MISSINGRELATIVES (Search for the missing unicellular relatives of animals)
Okres sprawozdawczy: 2023-07-01 do 2025-12-31
Our project seeks to solve a fundamental mystery: how did the first animals evolve from their single-celled ancestors? This question is not just about the past; it's key to understanding our own biology, from how our bodies are built to the origins of diseases like cancer.
There has been a lot of work in the last two decades from diverse unicellular relatives of animals to understand the transition. In particular, there has been work on 4 different unicellular linages. Work on those species have demonstrated that
the unicellular ancestor of animals had a larger repertoire of genes associated with multicellularity than previously thought. These include “animal-specific” genes such as protein tyrosine kinases, integrins and Brachyury. This suggests a latent genetic potential in place at the origin of animals and hints at a much more gradual transition in their emergence. However, a comparison of extant early-branching animals and their unicellular relatives still reveals an abrupt difference between protists and the body plans of extant animals. This gap could be due to intermediate lineages going extinct, or that descendants of key lineages have not been found yet.
Recent DNA environmental surveys suggest the latter, revealing several novel kingdom-level lineages that branch close to animals and remain unknown. In particular, we know there are at least 8 unknown lineages closely related to animals. Any of those lineages could potentially change our perception on how animals originated. Indeed, there has never been a systematic, focused survey of animal's relatives. I propose to do this by exploiting recent developments in long-read metabarcoding. We will screen different environments and isolate these novel lineages using fixation-free labeling methods. We will culture as many as possible of them and get their genomes.
We will provide a complete picture of the diversity among animal relatives, which will also be relevant to ecologists. We aim to culture between 1 and 3 novel, unknown species and get the genomes of 4 to 6. These novel lineages will allow us to address fundamental questions about the origin of animals that cannot be answered with the current taxon sampling, including the origin of embryogenesis and spatial cell differentiation.
There has been a lot of work in the last two decades from diverse unicellular relatives of animals to understand the transition. In particular, there has been work on 4 different unicellular linages. Work on those species have demonstrated that
the unicellular ancestor of animals had a larger repertoire of genes associated with multicellularity than previously thought. These include “animal-specific” genes such as protein tyrosine kinases, integrins and Brachyury. This suggests a latent genetic potential in place at the origin of animals and hints at a much more gradual transition in their emergence. However, a comparison of extant early-branching animals and their unicellular relatives still reveals an abrupt difference between protists and the body plans of extant animals. This gap could be due to intermediate lineages going extinct, or that descendants of key lineages have not been found yet.
Recent DNA environmental surveys suggest the latter, revealing several novel kingdom-level lineages that branch close to animals and remain unknown. In particular, we know there are at least 8 unknown lineages closely related to animals. Any of those lineages could potentially change our perception on how animals originated. Indeed, there has never been a systematic, focused survey of animal's relatives. I propose to do this by exploiting recent developments in long-read metabarcoding. We will screen different environments and isolate these novel lineages using fixation-free labeling methods. We will culture as many as possible of them and get their genomes.
We will provide a complete picture of the diversity among animal relatives, which will also be relevant to ecologists. We aim to culture between 1 and 3 novel, unknown species and get the genomes of 4 to 6. These novel lineages will allow us to address fundamental questions about the origin of animals that cannot be answered with the current taxon sampling, including the origin of embryogenesis and spatial cell differentiation.
To get a clear picture of this major evolutionary transition (the origin of multicellular animals), we first need to identify all of our closest living unicellular relatives, many of which remain hidden in the world's oceans and lakes.
Aim 1.
Our first goal was to create a comprehensive map of the unicellular organisms that are most closely related to animals and detect any unknown group. Since many of these microbes have never been seen, the best way to find them is to use DNA. We search for their genetic fingerprints—traces of their DNA—directly in water samples collected from the environment.
Our progress so far:
-By analyzing vast public databases of environmental DNA, we have confirmed the existence of eight completely new lineages of organisms that are close relatives of animals.
-We have mapped the global distribution of these mysterious lineages, creating a "treasure map" that tells us the best places on Earth to find them.
-We have designed "Holozoa-specific" primers for the 18S RRNA. These will be primer that will preferentialy amplify the organisms of interest in the PCR and not bilaterian animals or other major eukaryotic lineages. We have tested them and they seem to work fine.
-We have also designed specific primers for all the eight unknown lineages we have so far detected.
-Following our map, we have already conducted sampling expeditions in promising locations, including the Mediterranean Sea, the Atlantic coast of the Iberian Peninsula, and Lake Sanabria in Spain. We are currently extracting DNA and performing PCRs to sequence those samples using universal primers and specific primers for our organisms that take most metazoans out (to increase chances to get organisms of interest).
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Aim 2.
Finding an organism's DNA is one thing; growing it in the lab is another major challenge. To truly study these new life forms, we need to cultivate them.
Our progress so far:
-We have been working on a method to make these organisms glow with fluorescence, which would allow us to study them while they are alive. While this technique is still under development for these new cell types, we have successfully established an alternative method that lets us see their unique shapes and structures, even though it kills the cells. We believe this will help us “fish” these unknown lineages-
-Using FISH-CARD we have the first images of two lineages that were previosuly unknown.
-Indeed, our most exciting breakthrough has been the successful isolation and cultivation of a representative from a new lineage, known as MAOP-2. We now have a thriving culture of this organism. This culture is pure and ready for in-depth genetic sequencing.
Aim 3.
With a new organism successfully growing in our lab, we have now begun the final and most exciting phase of our project: getting to know our newfound relative.
Our progress so far:
-We are currently performing advanced microscopy and cell biology experiments on our first isolate, the MAOP-2 lineage. This is our first chance to observe the behavior and structure of an organism closely related to animals that, until now, was completely unknown to science. The insights from these first studies will pave the way for a deeper analysis of its genome and its unique place on the tree of life.
-we also got a transcriptome and a genome.
Aim 1.
Our first goal was to create a comprehensive map of the unicellular organisms that are most closely related to animals and detect any unknown group. Since many of these microbes have never been seen, the best way to find them is to use DNA. We search for their genetic fingerprints—traces of their DNA—directly in water samples collected from the environment.
Our progress so far:
-By analyzing vast public databases of environmental DNA, we have confirmed the existence of eight completely new lineages of organisms that are close relatives of animals.
-We have mapped the global distribution of these mysterious lineages, creating a "treasure map" that tells us the best places on Earth to find them.
-We have designed "Holozoa-specific" primers for the 18S RRNA. These will be primer that will preferentialy amplify the organisms of interest in the PCR and not bilaterian animals or other major eukaryotic lineages. We have tested them and they seem to work fine.
-We have also designed specific primers for all the eight unknown lineages we have so far detected.
-Following our map, we have already conducted sampling expeditions in promising locations, including the Mediterranean Sea, the Atlantic coast of the Iberian Peninsula, and Lake Sanabria in Spain. We are currently extracting DNA and performing PCRs to sequence those samples using universal primers and specific primers for our organisms that take most metazoans out (to increase chances to get organisms of interest).
-
Aim 2.
Finding an organism's DNA is one thing; growing it in the lab is another major challenge. To truly study these new life forms, we need to cultivate them.
Our progress so far:
-We have been working on a method to make these organisms glow with fluorescence, which would allow us to study them while they are alive. While this technique is still under development for these new cell types, we have successfully established an alternative method that lets us see their unique shapes and structures, even though it kills the cells. We believe this will help us “fish” these unknown lineages-
-Using FISH-CARD we have the first images of two lineages that were previosuly unknown.
-Indeed, our most exciting breakthrough has been the successful isolation and cultivation of a representative from a new lineage, known as MAOP-2. We now have a thriving culture of this organism. This culture is pure and ready for in-depth genetic sequencing.
Aim 3.
With a new organism successfully growing in our lab, we have now begun the final and most exciting phase of our project: getting to know our newfound relative.
Our progress so far:
-We are currently performing advanced microscopy and cell biology experiments on our first isolate, the MAOP-2 lineage. This is our first chance to observe the behavior and structure of an organism closely related to animals that, until now, was completely unknown to science. The insights from these first studies will pave the way for a deeper analysis of its genome and its unique place on the tree of life.
-we also got a transcriptome and a genome.
The results will surely have implications to our understanding of how animals emerged and even how complex life evolves. We need to get more species into culture and more genomes.