I have been busy posting cytochrome P450 related items on my substack page I Dream of Genes. Check it out at davidrnelson.substack.com

I Dream of Genes | David R Nelson | Substack

The Cytochrome P450 Universe. Click to read I Dream of Genes, by David R Nelson, a Substack publication. Launched 2 months ago.

davidrnelson.substack.com

Check out Why we want to sequence the genescape of the universe" at davidrnelson.substack.com

I Dream of Genes | David R Nelson | Substack

The Cytochrome P450 Universe. Click to read I Dream of Genes, by David R Nelson, a Substack publication. Launched 9 days ago.

davidrnelson.substack.com

My new P450 substack at davidrnelson.substack.com is growing. I have made 7 posts in the last 4 days and more are in the works. Posts have 7-14 views in this few days.

David's Substack | David R Nelson | Substack

The Cytochrome P450 Universe. Click to read David's Substack, by David R Nelson, a Substack publication. Launched 3 days ago.

davidrnelson.substack.com

I have started a Substack davidrnelson.substack.com This is an experiment. We'll see how it works.

David's Substack | David R Nelson | Substack

My personal Substack. Click to read David's Substack, by David R Nelson, a Substack publication. Launched 3 hours ago.

davidrnelson.substack.com

I have identified 35 P450s in the Cephalopod Nautilus pompilius proteome found at figshare.com/articles/dat.... There are three new P450 families and a few unassigned CYP3 clan fragments. Blasting the genome showed the 3 clan fragments are part off some larger clusters that need assembly.

I have just finished annotating P450s from the Scaphpod mollusc Pictodentalium verdenei a tusk shell mollusc. This is the first genome from that molluscan class so it had 18 new CYP families and an amazing 280 P450 seqs. much larger than typical animal species with about 85-100 P450s.

Recently I have been annotating P450s from molluscs. After 19 genomes in gastropods, it appears we are close to saturation in that group. Molluscs have 8 clades, so more to go. 83 new families were named from molluscs.

Blue because NCBI's site is down

This paperbush started out with three flowers on Feb 2021. I had covered it with an ad hoc green house made of storm windows and kept it from freezing with 5 gal heated water buckets for 10 days when we had a hard freeze.

This is an American paperbush in our backyard. It blooms now (Jan Feb) and the aroma is very sweet and strong as the flowers slowly open into yellow spheres.

In Memphis we are preparing for our annual Charles Darwin birthday party. We started these when he was 199. Now he is 216 so 18 years worth of parties. (Missed 2020). Invited about 60 people. Waiting for the primordial soup (gumbo) and trilobites (meatballs in Stubb's original BBQ sauce).

One new P450 gene CYP3K2 from the velvet worm Epiperipatus broadwayi is more than 1.1 Mb. This may be a record for a P450 gene. They are only about 500 amino acids long. This gene is still missing the last exon. The intact ortholog is CYP3K2_Principapillatus_hitoyensis GKOM01016447.1 from TSA.

Velvet worms are a distinct phylum of animals in the panarthropods. I have been annotating P450s from genome of Epiperipatus broadwayi and indirectly the TSA transcripts of Principapillatus hitoyensis. I am seeking to find and name all P450 families on earth. This genome has 5 new P450s families.

There is a deep sea worm in the Hemichordates that has been named YODA.

Phoronida are a phylum of animals (horseshoe worms) with only 13 named species. I have annotated 62 P450s from Phoronis australis (30 P450 families). I need more to achieve saturation (finding all P450 families).

Cycliophora is an animal phylum with 2 named species. They live on the lips of lobsters. I have 5 seqs from one species, clearly not done yet with this curious animal. Anyonwe have a transcriptome or genome?

Micrognathozoa is an animal phylum with only one species Limnognathia maerski. There is an SRA dataset for this species and I have mined out two P450s by walking the SRA reads CYP20GN1 and CYP51A1. There are more P450s but it is too hard to assemble them by walking the reads.

Small animal genomes are hard to sequence because they have very little DNA. To get enough DNA for typical methods would require many organisms and that creates problems with heterozygosity. Single cell methods are transforming this area so maybe we can get seqs for these rare creatures.

Loriciferans are a small animal phylum with 29 named species. I was able to get one transcriptome from Maria Herranz. I found 7 families and 15 P450 seqs. We do not know if this is saturated yet, but probably not. Need more transcriptomes or genomes.

Dicyemida is a phylum of parasitic animals of cephalopod molluscs that live in the kidneys. There are seqs of P450s reported from dicyemids but they have high sequence identity to the octopus host and are probably contamination. This may be the only animal to have zero P450s.

Placozoans have only 4 named species and another unnamed species. I have named all the P450s from 3 of the 4 named species. I believe I have found all 18 P450 families in this phylum (saturation).

Amphioxus species are a key evolutionary phylum of early chordates. In seeking the saturate the amphioxus clade I have downloaded the genome of Asymmetron lucayanum. I found 817 contigs with P450 seqs. 1898 exons were identified and it looks like no new families wiil be found vs. Branchiostoma.

Mud dragons make up the Kinoryncha phylum of animals. These marine sediment animals are about 1 mm long and are found all over the world. I have annotated all the P450s from 18 transcriptomes shared with me by Maria Herranz. This is a total of 3868 P450s. 63 families were found. Saturation!

I have joined with the Weed Genomics Consortium to annotate P450s from approximately 50 weed genomes. So far I have named the P450s from 31 weed genomes. papers are in the pipeline.

I just deactivated my X account.

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