I'm seeking for a gene that can be used to differentiate between C. ljungdahlii, C. autoethanogenum and C. ragsdalei. As far as I know from whole genome sequencing data, they have identical 16S and 23S genes. ITS regions also vary within the multiple rRNA operons those cells have so it is not a good choice.
I checked complete genome sequences for autoethanogenum and ljungdahlii to find candidate genes to differentiate among them, but could not find acces to ragsdalei data apart from the 16S rRNA gene.
I'm also having a similar problem with C. carboxidivorans and C. scatologenes.
Any help will be welcome.
Quizás sería bueno que utilizaras enzimas de restricción para el ITS secuenciado. Hay programas informáticos que te ayudarán a ello. http://www.restrictionmapper.org/
Gracias Gustavo,
también probé con ITS, no parece ser un buen marcador. En los Clostridium que me interesan hay regiones ITS en los múltiples operones SSU que tienen en el genoma y las secuencias dentro de una única especie no coinciden. Estoy ahora explorando con gyrA o gyrB.
Un saludo
C. ljungdahlii and C. autoethanogenum are basically the same organisms the second carries multiple deletions in the chromosome. I don't know about C. ragsdalei but you may want to check the chaperonin 60 (cpn60) sequences
Hill et al 2004 cpnDB: a chaperonin sequence database. Genome Res 14: 1669–1675.
Jian et al 2001. Int J Syst Evol Microbiol 51:1633–1638.
Verbeke et al 2011 Syst Appl Microbiol 34: 171–179.
Goh 1997 J Clin Microbiol 35: 3116–3121.
Suerte