To generate a pilot genetic tree in PATRIC, you can upload genomes to the service individually as the service allows you to include as many as 200 genomes, having them one by one would be attacked tedious. So we're going to make a few groups of genomes to facilitate adding them to a phylogenetic tree. For this particular exercise, we're going to look at endosymbiotic bacteria insects. Let's start with Buchnera, a genus of bacteria that lives with them selves of Aphids. It's generic name honors Paul Buchner who's regarded as the founder of systematic simbiosys research. So let's go to the global search button here on the home page and we type in Buchnera here in the global search box, and you can either hit Return or click on the search icon. This will overwrite the page to show you the results of your search function and that will be broken down into several different categories. Genomes, genomic features, taxa and specialty genes. Right now, I'm interested in going to the genus. So I'm going to hit Buchnera here and click on that. That will rewrite the page and show me the landing page for the genus. You can see that this landing page we try to bring in a lot of different information across the top is a breadcrumb that shows us where we are in the taxonomy of the organism. And then you'll notice that there are several tabs across the top and few of these will be getting into today. This is the information about this particular genus that's available at NCBI. These are the reference and representative genomes for this particular group and we also have the metadata that we try to show what kind of metadata is available for the group itself. We're going to talk about phylogeny in more detail soon. So let's skip over that. If I were to click on the taxonomy tab here, that would show me the species that are known with this particular genus and you can see it's only one and let's click on genus. This will show all the genomes that are within the genus Buchnera and it's going to include my private data with the public data. If I was logged out, it would only show me the public data. When you're logged in, you'll see both your private and public data. Let's click up here on the Filters and that opens a dynamic filter at the top where you can refine your search. Under Public, let's click on True. I don't want it include any of my private genomes in this tree. So I click on True. And now, I can see that there are 99 total genomes. Let's look under genome status. There are complete genomes and what is a complete genome? It means that the genome has been sequenced and the assembly is consistent with the number of chromosomes, and plasmids that are available in the organism in the strain itself. For example, if there's one complete chromosome and one class and that there would be two, what we would call contegs and that all the ends are totally resolved. We all know what a plasmid sequenc is and WGS stands for whole genome shotgun, and this is a genome where the contegs do not equal the amount of chromosomes and, or plasmids in the genome and the ends, probably haven't been resolved. Let's click on complete, okay? because these should be higher quality genomes. And you can see here, it says there are 64 of them. So I like this group. It looks like a good group. It's got a bunch of different hosts that it comes from a bunch of different countries, different years. And more important, all the genomes are of good quality. Actually, all of the metadata characteristics are important. I want to create a group of these. How do I go about it? Well, right here, here's genome name in this check box just to the left of that. If you click on that, it's going to select all of them simultaneously. And notice something else that it does. Within this vertical green bar, it populates it with possible downstream functions. I'm going to click on the group icon here. This opens a pop-up window where I can add ginos to a group that I already have or I can create a new group. To create a new I click on the down arrow here and click New Group. And now what remains as I have to name the group and I'm going to call it who Buchnera May2020 because that's when I'm creating this group. I'm just going to add it. And you notice that a pop up window comes up that says that group has been created. So I've created my first group for this analysis. And now, I want to create more that was so great. I want to create some more groups and I'm going to go step outside of Buchnera. I want to look at the other genomes that are close to them. So how can I find that in patch drive to read papers and look up the taxonomy and look who's close to them? Well, yes, that's always a good thing to do, but let's go to this phylogeny tab here and maybe we can get there a little quicker rather than reading all the papers. So we click on the phylogeny tab. And this opens up an order level tree for the enterobacteriales. And what we did, several years ago was got what we consider to be the high quality genomes within this order. And you can tell there are a bunch of them so that people could see who is close to a particular genus or species. So how do I find Buchnera and all of this? I'm just going to go the Ctrl+Find, going to put in Buchnera, hit return and we have to click down a bit. There we go. Here's our Buchnera. So here's Buchnera here. They're all the Buchnera. What's interesting about most of the insect in those symbionts is you notice their names are really long and complicated. The first part is the name of the bacterium, the second part here is the name of the host. So when it's something that's as closely aligned with the host is these endosymbiotic bacteria on they've decided to combine the names here. So we have Buchnera all the way down and then the first place we get outside of Buchnera is here with this Candidatus Riesia. You notice this little period at the end of the line here, let's click on that. And you notice when I click on that, the vertical green bar over here to the right is populated with some downstream functions. This time I want to go to the genome, so let's click on genome. And this is going to open the landing page for this particular genome that we have. But I want to see if there are more of these in Patrick. Along the Breadcrumb, this is the particular strain. This is the species here, Riesia pediculicola, or we can go to the genus. So let's click on that. While that loads, let's talk a little bit about this organism. Riesia is named for Eric Wright, who first comprehensively investigated the endosymbiotic system in lines. So these are the endosymbiotic bacteria that are found within the Laos and in the humans they are head lice, body lice, and pubic lice, and we have data for all of those genomes and Patrick. So you've already seen how they do this in Buchnera, we would click on the genomes. And then let's click on this filters again. And let me point out that all of them are public genomes and we have complete whole genome shotgun and plasmid. And one thing I didn't tell you when we created the first group is the code on trees algorithm works on shared proteins. If you choose a class that plasmids are one, generally small and two, they don't have many genes on them that are shared broadly. Often these genes are unique. Building a tree with plasmids is generally a bad idea, so I don't want to do it, I'll click on the complete genome. And in this case, because there was only one complete one, I'll click on WGS which stands for whole genome shotgun. So let's click on that too. So that gives me eight total genomes. I'm going to click here and the check box to select all of them and look, it's kind of a nice collection. We've got these different hosts. It looks like somewhere isolated from gorillas, some from pubic lice. I think this is from an orangutan and this is from the header body While skin humans. So let's click on the group to create a new group. Once again, it opens up a window. I want to create a new group and I'm going to call this Ricia May 2020, and we click on add. Now we can do that and let's watch down here at the corner and it says, you've created a new group, hurray. Well, let's do another one that was so much fun. Let's go back to the tree so we need to click on this other tab here and we go back to the tree. And the next one down is this one that says Wigglesworthia. So let's click on this again. And now it's selected and we can go to the genome. But let me point out that blockmonia is the next one down because next time we're going to try the global search function for that Gmail. So, I want to go to the genome page for that. And once again, remember this is for one single genome within this genus and species, but I want to find out how many genomes Patrick has four Wigglesworthia. Yeah, and Wigglesworthia, let me point out was named first Sir Brian Wigglesworth, a British entomologist who made significant contributions to the field of insect physiology. These bacteria are fascinating. They found in tsetse flies, which are the vectors of African sleeping sickness. So let's click on the breadcrumb that takes me to the genus within the breadcrumb, which is where those Wigglesworthia here. So let's click on that. This gives me all the information about this organism. And let's click on genomes here. Now I know that some of these are my own private genomes because, actually, like Wigglesworthia, I think it's interesting. And tsetse flies are fascinating. You should read more about them. They only give birth to one larva a year. They're just amazing insects, so let's click on the filters, and I want just the public genomes, not my private genomes, I'm going to click on true. And then we're going to create a group of Wigglesworthia so we click here. And then we click on, once again, the group icon and we're going to create a new group. I'm going to call it Wigglesworthia May 2020, and add that group and we watched down here and see that we have successfully created the group. And one more, remember we wanted to do blockmonia. So instead of going to the homepage in the global search, you're going to the tree and walking through there. Let's enter blockmonia in the global search page, might just hit return. And once again, the search results start with genomes genomic features, and then taxa, and this will take me right to the genus. Now, notice slip, it says Candidatus. Candidatus means that the taxonomy committee hasn't approved it yet. But the proposed name of this genus honors the zoologist Friedrich Blackman. Back in 1880s, he found these unusual bodies in the mid guts of ants, and then later of course because we didn't know how to do this at that time, those were discovered to be bacteria. That's why they've named this for him. I just love the way that these things are named in that it honors scientists who along time ago were doing a lot of hard work to figure out what was going on in different organisms. Let's click on the genomes tab. Let's click on the filters here to see if any of that data is private or not. They all seem to be public data. Often when these things are blank, it could be a private data, but I haven't annotated any of these genomes independently, so I want to create my last group, I click here. And then I go to the group icon. I want a new group, and that is Blockmonia May 2020. And ad that group and then once again we see it right there, okay. We have four groups were ready to launch the code on trees job. Join me in the second instructional video where I'll show you how to add those four groups and private genome. Okay, it's time for your first assignment with code on trees and that is creating genome groups. I want you to create five groups. Brucella, the representative Genomes brucella isolated from frogs. If you go into the genomes tab, there's a text box above the table. And you could put something like frog in it, and filter the table down just a little hind. Brucellaceae which is a group that contains the brucella and also the okra back room. There is a breadcrumb on top of the NCBI Taxonomy at the top of the brucella page. And you can March your way up that to get to that particular taxonomic grouping. Bartonella, bartonella has representative and reference genomes. I want you to create one group that has both, and mesorhizobium has representative and reference genomes. I want you to create one group that has both. Now, you may have to go into global search to look for something like mezorhizobium. Because it's not a pathogen group. In generally Patrick has under organisms has dropped down for well known pathogens that are of interest to MIH and. Mezorhizobium is not generally a pathogen group, but you can find it by using the global search function. So create those groups and then we're going to build some trees. Thanks.
