Comments on: Two classical maize genes, synteny, and the mystery of the missing gene http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/ Genetics: Studying the Source Code of Nature Thu, 12 Jan 2012 03:50:37 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: James http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-5512 James Sun, 09 May 2010 17:23:36 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-5512 Purple corn kernels are purple because they contain lots of a pigment called anthocyanin. The genes that can make corn more purple are the ones that control the production of the anthocyanin pigment. The four classical genes involved in this process, although there are also others, are C1 (colored aleurone1), Pl1 (purple plant1), B1 (colored plant1), and R1 (colored1). Please let me know if you're like to know more. Purple corn kernels are purple because they contain lots of a pigment called anthocyanin. The genes that can make corn more purple are the ones that control the production of the anthocyanin pigment. The four classical genes involved in this process, although there are also others, are C1 (colored aleurone1), Pl1 (purple plant1), B1 (colored plant1), and R1 (colored1). Please let me know if you’re like to know more.

]]> By: yefta http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-5511 yefta Sun, 09 May 2010 14:38:02 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-5511 can u tell me about purple gen in maize? or purple gen controlled in maize.... Thank you a lot can u tell me about purple gen in maize? or purple gen controlled in maize…. Thank you a lot

]]> By: James http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-4995 James Mon, 08 Mar 2010 23:12:18 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-4995 That's the problem with working with in-house tools. I take WAY too much for granted with trying to explain an image like this to people outside of my own lab. That’s the problem with working with in-house tools. I take WAY too much for granted with trying to explain an image like this to people outside of my own lab.

]]> By: Noah Fahlgren http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-4994 Noah Fahlgren Mon, 08 Mar 2010 22:57:27 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-4994 Cool. Yeah, I wasn't sure if the search had only included gene models or the whole genome sequence. Definitely sounds like the gene is not there then. Cool. Yeah, I wasn’t sure if the search had only included gene models or the whole genome sequence. Definitely sounds like the gene is not there then.

]]> By: James http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-4992 James Mon, 08 Mar 2010 22:31:41 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-4992 That's a cool discovery Haibao. Genes like C1 and Pl1 are interesting, but it's fascinating to learn about genes controlling traits that are actually important to feeding people. Would it be equally parsimonious to theorize that the gene was gained (or at least transpositioned) into it's current location in in the rice-brachypodium lineage, and then became non-functional in rice vs being present in the ancestor of all grasses and then getting lost in sorghum and broken in rice? Each has two changes, but gene gain might be considered a bigger change than gene loss. That’s a cool discovery Haibao. Genes like C1 and Pl1 are interesting, but it’s fascinating to learn about genes controlling traits that are actually important to feeding people.

Would it be equally parsimonious to theorize that the gene was gained (or at least transpositioned) into it’s current location in in the rice-brachypodium lineage, and then became non-functional in rice vs being present in the ancestor of all grasses and then getting lost in sorghum and broken in rice? Each has two changes, but gene gain might be considered a bigger change than gene loss.

]]> By: James http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-4991 James Mon, 08 Mar 2010 22:10:54 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-4991 The final search was done against the whole genomic sequence. Normally we mask non-coding sequence (the purple regions of the first four panels, but when we can't find the gene we default to repeat masked genomic sequence, and in this case I manually switched to completely unmasked sequence. So if there was any sequence in the region similar enough to qualify as a blast hit, we should be able to see it. If I switch to blastn ( http://tinyurl.com/yzmdz8j ) there are two hits within the region, but one is 24 bp long and the other 19. This dataset definitely can be used to identify missing or incomplete gene models. For example you can easily tell the brachy ortholog of the maize P1 gene is truncated, here: http://synteny.cnr.berkeley.edu/wiki/index.php/Classical_Maize_Genes_Examples#Pericarp_color1_and_Pericarp_color2.2C_local_duplicate_genes The final search was done against the whole genomic sequence. Normally we mask non-coding sequence (the purple regions of the first four panels, but when we can’t find the gene we default to repeat masked genomic sequence, and in this case I manually switched to completely unmasked sequence. So if there was any sequence in the region similar enough to qualify as a blast hit, we should be able to see it. If I switch to blastn ( http://tinyurl.com/yzmdz8j ) there are two hits within the region, but one is 24 bp long and the other 19.

This dataset definitely can be used to identify missing or incomplete gene models. For example you can easily tell the brachy ortholog of the maize P1 gene is truncated, here:

http://synteny.cnr.berkeley.edu/wiki/index.php/Classical_Maize_Genes_Examples#Pericarp_color1_and_Pericarp_color2.2C_local_duplicate_genes

]]> By: Noah Fahlgren http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-4990 Noah Fahlgren Mon, 08 Mar 2010 21:44:44 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-4990 Is it possible the gene model is missing? I think I pulled up the equivalent region (http://www.brachybase.org/cgi-bin/gbrowse/brachy8/?name=Bd1:44873086..44965627) at my colleagues site brachypodium.org. They sequenced the transcriptome and have a transcript assembly pipeline that identifies splice junctions and builds exons. It does look like there are some small transcribed regions in the "gap," nothing obvious though. Is it possible the gene model is missing? I think I pulled up the equivalent region (http://www.brachybase.org/cgi-bin/gbrowse/brachy8/?name=Bd1:44873086..44965627) at my colleagues site brachypodium.org. They sequenced the transcriptome and have a transcript assembly pipeline that identifies splice junctions and builds exons. It does look like there are some small transcribed regions in the “gap,” nothing obvious though.

]]> By: Haibao Tang http://www.jamesandthegiantcorn.com/2010/03/08/two-classical-maize-genes-synteny-and-the-mystery-of-the-missing-gene/comment-page-1/#comment-4989 Haibao Tang Mon, 08 Mar 2010 21:33:16 +0000 http://www.jamesandthegiantcorn.com/?p=1508#comment-4989 this is interesting, James.. we tracked down a soft grain trait gene in wheat and brachy and found there is only gene relic in rice, and totally gone in sorghum. so that'd be a loss in the sorghum lineage. http://mbe.oxfordjournals.org/cgi/content/full/26/7/1651 In your case it looks like a loss is in the brachy lineage. to me, it seems that many cereal traits (that humans value) have quite narrow phylogenetic context. this is interesting, James.. we tracked down a soft grain trait gene in wheat and brachy and found there is only gene relic in rice, and totally gone in sorghum. so that’d be a loss in the sorghum lineage.

http://mbe.oxfordjournals.org/cgi/content/full/26/7/1651

In your case it looks like a loss is in the brachy lineage. to me, it seems that many cereal traits (that humans value) have quite narrow phylogenetic context.

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