Supplement material

Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology

Stefanie Wehner, Gopala K. Mannala, Xiaoxing Qing, Ramakanth Madhugiri, Trinad Chakraborty, Mobarak Abu Mraheil, Torsten Hain and Manja Marz

Overview

Used genomes
Annotations for L. monocytogenes
Detected/Predictes sRNAs
Transcription of selected long asRNAs (lasRNAs) (Fig. 3)
Transcription of selected long asRNAs (lasRNAs) with primer products
Transcription of selected long asRNAs (lasRNAs) (including dPrfA)
Chromosomal loci of selected long asRNAs (lasRNAs) in L. monocytogenes 1/2a EGD-e, L. monocytogenes 1/2a 10403S and L. monocytogenes 1/2a EGD
Transcription of selected long asRNAs (lasRNAs) in L. monocytogenes 10403S

Genomes

Organism external Link
Listeria_monocytogenes_ATCC_19117_uid175109 Download link
Listeria_monocytogenes_Clip80459_uid59317 Download link
Listeria_monocytogenes_EGD_e_uid61583 Download link
Listeria_monocytogenes_FSL_J1-208 Download link
Listeria_monocytogenes__serotype_1_2b_SLCC2755_uid52455 (NC_014495) Download link
Listeria_monocytogenes__serotype_1_2b_SLCC2755_uid52455 (NC_018587) Download link
Listeria_monocytogenes_serotype_4a_L99_uid161953 Download link
Listeria_monocytogenes_serotype_7_SLCC2482_uid174871 (NC_018591) Download link
Listeria_monocytogenes_serotype_7_SLCC2482_uid174871 (NC_018888) Download link
Listeria_monocytogenes_SLCC2372 (NC_018588) Download link
Listeria_monocytogenes_SLCC2372 (NC_018889) Download link
Listeria_monocytogenes_SLCC2376_uid175111 Download link
Listeria_monocytogenes_SLCC2378_uid175105 Download link
Listeria_monocytogenes_SLCC2479_uid175108 Download link
Listeria_monocytogenes_SLCC2540_uid175106 Download link
Listeria_monocytogenes_SLCC7179_uid175107 Download link


Annotations for L. monocytogenes

ncRNA class gff
ribosomal RNAs rRNAs.gff
transfer RNAs tRNAs.gff
other ncRNAs ncRNAs.gff


Predictes sRNAs


All candidates

Candidates overlapping sRNAs previously described in literature and Rfam

Candidates overlapping only with Rfam predictions

Candidates antisense to protein-coding genes

New sRNA candidates

Primers used in this study


Primers

Transcription of selected long asRNAs (lasRNAs) (Fig. 3)


Internalin protein (Fig. 3A) | (eps)

Internalin protein (Fig. 3B) | (eps)

novel long antisense transcript (Fig. 3C) | (eps)

predicted SAM-dependent methyltransferase (Fig. 3D) | (eps)

rRNA methylase homolog (Fig. 3E) | (eps)

similar to a methylated DNA cystein methyltransferase (Fig. 3F) | (eps)

kdpABCD (Fig. 5) | (eps)

Transcription of selected long asRNAs (lasRNAs) with primer products


Internalin protein (Fig. 3A) | (eps)

Internalin protein (Fig. 3B) | (eps)

rRNA methylase homolog (Fig. 3E) | (eps)

similar to a methylated DNA cystein methyltransferase (Fig. 3F) | (eps)

kdpABCD (Fig. 5) | (eps)

Transcription of selected long asRNAs (lasRNAs) (including dPrfA)


Internalin protein (Fig. 3A) | (eps)

Internalin protein (Fig. 3B) | (eps)

novel long antisense transcript (Fig. 3C) | (eps)

predicted SAM-dependent methyltransferase (Fig. 3D) | (eps)

rRNA methylase homolog (Fig. 3E) | (eps)

similar to a methylated DNA cystein methyltransferase (Fig. 3F) | (eps)

kdpABCD (Fig. 5) | (eps)

Chromosomal loci of selected long asRNAs (lasRNAs) of L. monocytogenes 1/2a EGD-e, L. monocytogenes 1/2a 10403S and L. monocytogenes 1/2a EGD


(illustated using Geco Software (80% identity, 90% coverage)

Internalin protein (Fig. 3A) | (pdf)

Internalin protein (Fig. 3B) | (pdf)

novel long antisense transcript (Fig. 3C) | (pdf)

predicted SAM-dependent methyltransferase (Fig. 3D) | (pdf)

rRNA methylase homolog (Fig. 3E) | (pdf)

similar to a methylated DNA cystein methyltransferase (Fig. 3F) | (pdf)

kdpABCD (Fig. 5) | (pdf)

Transcription of selected long asRNAs (lasRNAs) in L. monocytogenes 10403S


Internalin protein (Fig. 3A) | (eps)

Internalin protein (Fig. 3B) | (eps)

novel long antisense transcript (Fig. 3C) | (eps)

predicted SAM-dependent methyltransferase (Fig. 3D) | (eps)

rRNA methylase homolog (Fig. 3E) | (eps)

similar to a methylated DNA cystein methyltransferase (Fig. 3F) | (eps)

kdpABCD (Fig. 5) | (eps)