How to annotate the rps12 gene in chloroplast genome?

Question

[799591829]

Can someone tell me how to annotate the trans-splicing gene names "rps12" in chloroplast genome? Thanks!

[natasha.sernova]

It’s a common problem with this gene:

See these papers:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347418/ “For example, rps12 is a trans-spliced gene containing three exons in the angiosperm chloroplast genome. The first exon is located ∼30 kb upstream of the second exon, and on the opposite coding strand. The initial parsed record for the gene contained many other genes nested in the intron region. After the filtering step, those nested genes were dissociated from the name ‘rps12’ and assigned to their appropriate names. If no gene name was found, the feature was deemed to be an ‘ophan’ and assigned a local name (starting with ‘lcl_anno’).”

http://www.nature.com/articles/srep21669 “In addition, a total of 17 genes in A. membranaceus chloroplast genome have only one intron (Table S1); ycf3 is the only with two introns. Similarly, introns in the 3′-end of rps12, a trans-splicing gene are also absent. Moreover, the accD gene of A. membranaceus encodes a protein with 451 amino acids, which is shorter than the other accD proteins (Fig. S1)”.

http://ogdraw.mpimp-golm.mpg.de/ssi_faqs.shtml “ gene join(132071..132213,132214..133176,133177..133245, 133246..134308,134309..134775,134776..135828, 135829..136072,136073..137891,137892..138153) /gene="nad7" When OGDraw encounters a gene annotation like above, it assumes that the gene is trans-spliced, as this annotation style is normally used only for trans-spliced genes (like rps12). Accordingly, the gene will be separated into it's sublocations which will be drawn on the map as discontinuous, independent features.” http://www.ddbj.nig.ac.jp/sub/example-e.html DEFINITION Psilotum nudum chloroplast DNA, complete genome. FEATURES Location/Qualifiers source 1..138829 /cultivar="Kingyoku" /mol_type="genomic DNA" /organelle="plastid:chloroplast" /organism="Psilotum nudum" ---- omitted ---- CDS join(complement(68922..69035),133880..134137) /codon_start=1 /note="trans splicing of 5'rps12 exon and 3'rps12 exon" /product="ribosomal protein S12" /protein_id="BAB84240.1" /trans_splicing /transl_table=11 /translation="MPTIQQLIRNARQPIRSRTKSPALRG CPQRRGVCIRVYTTTPK KPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVSVRGGRVKDLPGVRYHIVRGT LDAVGVKDRKQGRSRYGVKKPK" exon complement(68922..69035) /gene="rps12" /note="5'rps12 exon, trans splicing" /number=1 /product="ribosomal protein S12" ---- omitted ---- exon 133880..134137 /gene="rps12" /note="3'rps12 exon, trans splicing" /number=2 /product="ribosomal protein S12" ---- omitted ----

The same is here, from another source: https://standage.github.io/is-refseqs-arabidopsis-annotation-tair10.html DEFINITION Psilotum nudum chloroplast DNA, complete genome. FEATURES Location/Qualifiers source 1..138829 /cultivar="Kingyoku" /mol_type="genomic DNA" /organelle="plastid:chloroplast" /organism="Psilotum nudum" ---- omitted ---- CDS join(complement(68922..69035),133880..134137) /codon_start=1 /note="trans splicing of 5'rps12 exon and 3'rps12 exon" /product="ribosomal protein S12" /protein_id="BAB84240.1" /trans_splicing /transl_table=11 /translation="MPTIQQLIRNARQPIRSRTKSPALRG CPQRRGVCIRVYTTTPK KPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVSVRGGRVKDLPGVRYHIVRGT LDAVGVKDRKQGRSRYGVKKPK" exon complement(68922..69035) /gene="rps12" /note="5'rps12 exon, trans splicing" /number=1 /product="ribosomal protein S12" ---- omitted ---- exon 133880..134137 /gene="rps12" /note="3'rps12 exon, trans splicing" /number=2 /product="ribosomal protein S12" ---- omitted ----

Answer 1

[natasha.sernova]

See page 4 in this paper, for example:

Finding the Core-Genes of Chloroplasts

http://arxiv.org/pdf/1409.6369.pdf

or this paper:

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057607

A citation from the article above: "Similar to the Nicotiana tabacum [48] and Panax ginseng [47] cp genomes, the Salvia miltiorrhiza cp genome has 18 intron-containing genes, 15 (nine protein-coding and six tRNA genes) of which contain one intron and three (clpP, rps12 and ycf3) of which contain two introns (Table 2). The rps12 gene is a trans-spliced gene with the 5′ end located in the LSC region and the duplicated 3′ end in the IR regions."

Have a look at this Nature-article:

Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus

http://www.nature.com/articles/srep21669

"In the present study, we have: (1) sequenced the chloroplast genome of A. membranaceus; (2) annotated the chloroplast genome; (3) identified SSR and tandem repeats of the genome; (4) carried out a phylogenetic analysis of the 38 chloroplast genomes based on 67 conserved proteins; (4) compared the structures of 13 chloroplast genomes in Papilionoideae; (5) identified genes that have been lost among the 36 chloroplast genomes in Papilionoideae subfamily; and (6) identified five hypermutation loci that can potentially serve as markers to distinguish A. membranaceus varieties. Our results have laid the foundation for future studies on the evolution of chloroplast genomes of legumes, as well as the molecular identification of A. membranaceus varieties."

This is an article describing chloroplast database:

ChloroplastDB: the Chloroplast Genome Database

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347418/

See also this posts:

Gene Set(S) For Gene Predictor Training

How To Annotate Parts Of Chloroplast Dna?

How can I use BLAST to extract chloroplast sequences from DNA reads?

Downloading rice chloroplast genome

What plant are you interested in, by the way?