 Our next speaker is Huaijin Zhou from UC Davis. We're going to continue on the theme of avians, but now talk about functional annotation, I think, and also coming from the perspective of now the USDA and agriculture as well. All right. Thanks for the invitation, and it's my great honor to share some of the recent data generated from a fan community. And I really like to switch the gear from DNA sequencing to the epigenome and regular elements. What does regulatory innovation in vertebrates actually? This is my first attempt to try to do in the comparative genomics. So I'm not really in the area of the comparative genomics. So I tried to give some of the specific examples about what are we learning about comparative epigenome. For the people who are not familiar with agricultural species, I'd like to provide some of the need of a background about the agricultural species. Chicken actually is the first agricultural species to be sequenced in 2004, because for the people in the comparative genomics know that chicken is really important if you look at the evolution phenogenetic tree. So it's a really important evolution point. And then later on, the cow and the horse in 2009 and pig in 2012 and sheep in 2014. Since those agricultural species were sequenced, there's a significant improvement in the economic important because of those information available to the community. You use the genomic connection and make significant improvement of those complex traits, such as milk production, growth rate, feed efficiency, and disease. And then if you think about for the livestock, agricultural species really have lots of the advantage. If you think about those livestock species have really abundant of phenotype in different environment, and they have a really good category information. So you really can utilize those phenotype and then use the genotype to predict the phenotype. And then animals, basically, if you try to think about personalized medicine in the biomedical field, so a really animal can be raised in a really different type of environment or control environment. So you can really evaluate genotype by environment. So you can really accurate predict the phenotype. So you can really evaluate them like pharmaceutical drugs in terms of what type of drug can be a really treat different type of disease. So livestock species really great model to us to understand the function of the specific genes. And then because all of those complex traits, very importantly, we know the contribution of these. It's not just the coding gene. Actually, the majority of these contributions by the non-coding variants. So there's many of the studies, many of the GWAS study in the biomedical field that demonstrate that the non-coding variants are very, very important for the contribution of the phenotypic variation in complex traits in closed disease. And then the reason of the study in both of the human and livestock do indicate those costive variants that are enriched in the regular regions. And then we know for whatever highly conserved those regular animals, such as an enhancer, all reasonably involved those enhancers do have different phenotypic consequence. So that's why it's important to doing the comparative epigenomics to learning about which kind of the regular animals are more highly conserved or reasonably involved. As we can see for the biomedical field, the people integrate of the genome-wide association results with the annotation from encode or roadmap of the epigenome are willing to provide a novel biological insights about the complex traits in humans, including the human disease. So basically, whatever from the biomedical field or the cultural and all the national science and foundation, most important things is talk about how we can use the genome to predict the phenome. So that's actually it's a black box between the genome and the phenome. What that is, the black box is actually gene-regulation. So that's how those regular animals play a very, very important role. And from this diagram, you can see basically that's involved lots of the regular animals, such as the promoter enhancer, insulator silencer, all of the together to basically form those complex regularity of the gene-regulation. And many of you guys familiar with this diagram from an encode to talk about unifying those cutting edge of the all-mix technology in order to identify, annotate those regular animals, whatever, the promoter enhancer, evaluate all chromatin assessability to understanding the function of the genome. So comparative genomics really provide really powerful tools to understand its function and biology based on the assumption of that connection between evolution of the conservation and the functional importance. So we think if they are functionally, if they are evolutionally conserved, that must be a very, very functional important. And then as we know, so for the human genome, if when the people did the comparative genomics, look at all of the vertebrates to find roughly 5% of those human genome are very conserved. And we know about the 1.5% of the human genome, it's a coding regions, which that means more than 70% of those conserved region in the non-coding region. That's indicated how regular animals are so important. So we learned a lot about the comparative genomics using DNA sequencing about the evolution in action. And we see a similar pattern, a similar trace for the evolution in action on the vertebrate epigenome. But there are some of the challenges as you can see. So when you do the comparative genomics using DNA sequencing, it's a one-dimension. But if you think about the epigenome, it's a really a multi-dimension of the information basically involved multiple tissues and multiple development stage. And then also multiple assays, such as a chip-seq and high C and a tachsic, so involve a huge amount of the information that integrated together to understand how the conserved or rapidly involved those regular animals in the genome. So now I'd like to bring about, introduce about the fan. It's a functional annotation of the animal genomes, why it's needed and what made an impact of these. So as many of the study indicated, those are the regular animals or functional animals really nest conserved compared to the coding sequencing, whatever between the species or between the different tissues or different development stage. And then this is the comparative, the fan work really can help us to understanding foundation of the biology. And then also especially when we work on whatever human disease or the economical traits in the livestock species, one of the most challenging is we have so many of the mutations variants, which one is a really costive variants. So this is an annotation of the animal genome, really can help us to improve the genomic synapse accuracy for those complex traits including the disease. And then obviously for the scientists we really want to understanding the monocular mechanism. So this will really help us to enunciate the monocular mechanism of those complex traits. And then obviously several of already mentioned how the livestock species are really great model physiologically, but also very important and they're really great model for the human health and disease traits. So like now I like to provide a very brief information about the fan. So in 2014, if you look at it here only roughly like 24 of the members contributed to the white paper at that time. And then past four to five years, so the member of the fan consortium already increased to 480 members. And similar to structure of the encode consortium, so we have a steering committee and also have a four different subcommittee, the animal sample and assay committee and the bioinformatics data analysis committee and metadata and data sharing committee and a community committee. So all of those four subcommittee really work together community communicated with the animal genome community to provide the standards, the assays and so the community can generate more of the resource for the communities. So for this fan community, so we basically provided those in central of the core assays. So obviously the RNA-seq is very, very important as it's a kind of the phenotype so there's a major phenotype of this and then a chromatin accessibility either use a DNA-seq or a TAC-seq and then this is a four histone modification mark. So if you look at it here, this is a four histone modification markers really can be used to identify either enhancer or promoters or silencers and then also the CDCF, it's a transcription factor can use to identify the insulator. And here just to provide some of the preliminary analysis, so basically we generated in the past few years compared to the human mouse with the data available. So if you look at it here, first on the two major tissues, so the spring at the liver and we use the H3K4 tri-methylation and H3K37 acylation indicated as an active promoter and I use H3K37 acylation and H3K4 monomethylation indicated as an enhancer. If you look at it here compared to all of the six species in terms of number of the promoters and number of the enhancer, they are pretty similar to each other in terms of the number of these. And then here we did the comparative analysis, look at the, called a sequencing conservation of in the promoters between the spring at the liver. If you look at it here basically, what does the sequencing conservation means? For example, if we look at in the cow, we have 10,000 of the promoters and we look at for this 10,000 of the promoters, how many of those promoters, those are sequenced in a nine ball in another species, but not necessarily there are active promoters. And you can see a number of these are reasonable. So basically among all of the mammals that are similar to each other, always the birds are much, much less conserved as expected. And then you will see those livestock accortual species. So they are pretty comparable in terms of their sequencing conservation between the mouth and the humans. And between the two different tissues are also very similar. And then if you look at the enhancer, sequencing conservation is the same thing you use a number of the enhancer and then to look at it in other species to see what are the percentage of those enhancer. So they have a sequencing conservation, not the functional conservation we are talking second. So for the sequencing conservation, probably you will notice between the promoter and the enhancer, they're pretty similar in terms of the percentage of the conservation. But if you look at the functional conservation, which means if you look at in the one species has tens out of the promoter or enhancers, and how many of these in other species also it's active promoter or enhancer. And you will see significant drop in terms of the percentage of these conservation in terms of whatever the promoter or enhancers between the, in the spring here. So you will see for the enhancer the percentage of these are significant next compared to the promoters. And then so we also try to do in another comparison, this is a final genetic tree across those six species. If you look at it here, basically we try to look at the compare ever two of the species they're near each other to see how many of those are conserved in terms of sequencing conservation. If you look at it here, look at the across all of the mammals, oh sorry, okay. So if you look at it here across all of the mammals, so there's 48 to 68% of these across the mammals are here. But if you look at the mammals, between the mammals and birds, only 26 to 45, and between the nether and a spring are pretty similar. And then, so if you look at the functional conservation and then you will see a significant drop. So if you look at it here, so you can see across the mammals only like 11 to 24% and then between the mammal and the bird only 5 to 8%. So this sequencing conservation versus functional conservation are significantly gonna change. Same thing for the spring. And if we look at those, what type of those genes nearby for those promoters for functional conservation, so you will see some of these like BCO receptor signaling cell cycling across all of the mammals. And then if you look at it between the mammal and the birds, you still see the BCO receptor and cell cycling and also the glycine, cyrcine. Let's look at the spring, if you look at the spring, you will see the similar of these BCO signaling. And then if you look at between the mammal and also the birds, you will see similar of the pattern of the cell cycle and BCO receptors. So we didn't see much of a difference in terms of between the nether and a spring. So they seem like have the similar of the conservation for the promoters. So let's look at the enhancers. If you look at the enhancers here, so you will see, so in terms of the, among all of the mammals, so it's 48 to 100%. And then if you look at the, between the birds and the mammal, it's 26 to 72 and similar to the spring. But if you look at the functional conservation, you will see the significant drop. Only have a 0.4 to 1%, and if you between the birds and the mammal, it's 0.04 to 0.1%. And if you look at the spring, spring is much, much higher, but still pretty low. And then if we look at the function of these, you will see that for the nether. And then, so this is the signal path where we needed more of a nether specific. And then still you can see the, like at both side of the signaling. And then if we look at the spring, you will see more of the tissue-specific, spring-specific involved more of the immune response, like B-cell receptor signaling, T-cell receptor signaling. And then you will see here the chem-kind signaling. And then as we have a chance to look at across all of the eight tissues, if you look at it here, you will see between the promoter and enhancer, obviously you can see within the mammal, it's higher than between the mammal and the birds, or also between the promoter and enhancer are significantly reduced. So here I can provide another example for the opening chromatin in those synaptic block. In the three of the examples between the chicken and the pig and cattle, so you will see that all appeared, all of those three species, but these only appeared conservative between the cattle and the pig and the cattle, but not as a chicken. And this is interesting. This is another example, basically conservative between the chicken and the cattle, but not in the pig. This is another example, basically about the tissue-specific, you can see they're conservative between the pig and the cattle, but not in the chicken. So some of the take-home messages, as you can see the sequelae conservation across the species was pretty similar between the promoter and enhancer, but functional conservation involved much, much faster than the promoters. And it appears the functional enhancer involved much rapidly in liver than in the spring, but not over the promoters. And then genes nearby the functional conservative enhancer are very enriched for those tissue-specific manner, but not in the promoters. And then if we choose the species of those appropriate of timescale of the conservation, we are allowed to study some of the specific of the constraints of the function. And then those are the regulatory and evolution analysis. The reality is just a knife stalk, a cultural species are a great model to understand the gene regulation in the humans. So I'd like to provide a few perspective in term of the challenging and the future direction. As mentioned about the reference genome, Eric's mentioned how important and the quality of this we consider a human mouse probably kind of tier one. And she can pick and cattle probably tier two in term of the quantity and the sheep or horse probably tier three. So this is a very important in term of doing the comparative genomics. And then especially doing the map of the coordinates of those regular elements across different species are really a challenge. Should we do in a synchrony similarity or positional conservation, it's a really, really challenge. And then, so here I wanna present just to look at the sequencing conservation and actually for epigenomics, you need to look at the density of those marks. You need it more quantitatively to look at how conserved between the different species, different tissues. And then also very important to understand especially the enhancer unit far away from the genes to understand which of the genes the enhancer unit target to understand functional elements of the promoter and enhancer interactions is very important. And it's really, really important to have more of epigenomic data and more diverse of the species, especially a cultural species. So we can understand more of the and can function or annotate of the animal genome to understand the biology. Without anecdote, thanks to all the people who contribute to all of those work here and as a funding agent from NIVA and industry. Thanks very much. So I think again, since we're running behind Harris, we're not gonna take any questions.