Where can I find sequences for V3 V4 reagions of borrelia?

Question

[agata88]

Hi all,

I would like to design primers for Borrelia and Babesia. I need only V3 and V4 regions of 16S.

Could you please tell me where can I download a reference sequence?

I was looking in greengenes and silva but I am not sure if results contain V3-V4 regions.

I would appreciate for help,

Best,

Agata

[GenoMax]

These are all Borrelia spp in NCBI 16S blast database

>gi|645321809|ref|NR_118689.1| Borrelia andersonii strain 21038 16S ribosomal RNA gene, partial sequence
>gi|645321807|ref|NR_118688.1| Borrelia japonica strain HO14 16S ribosomal RNA gene, partial sequence
>gi|343202919|ref|NR_043413.1| Borrelia garinii strain 20047 16S ribosomal RNA gene, complete sequence
>gi|219846283|ref|NR_025873.1| Borrelia turdi strain Ya501 16S ribosomal RNA gene, partial sequence
>gi|219846284|ref|NR_025874.1| Borrelia tanukii strain Hk501 16S ribosomal RNA gene, partial sequence
>gi|219846392|ref|NR_025983.1| Borrelia coriaceae strain Co53T 16S ribosomal RNA gene, partial sequence
>gi|636558650|ref|NR_114707.1| Borrelia bissettii strain DN127 16S ribosomal RNA gene, complete sequence
>gi|310974942|ref|NR_036806.1| Borrelia lusitaniae strain Poti B2 16S ribosomal RNA gene, partial sequence
>gi|310974943|ref|NR_036807.1| Borrelia valaisiana strain VS116 16S ribosomal RNA gene, partial sequence
>gi|636558488|ref|NR_114544.1| Borrelia coriaceae strain Co53 16S ribosomal RNA gene, partial sequence
>gi|219857192|ref|NR_024820.1| Borrelia turcica strain IST7 16S ribosomal RNA gene, partial sequence
>gi|219846271|ref|NR_025861.1| Borrelia miyamotoi strain HT31 16S ribosomal RNA gene, partial sequence
>gi|636559150|ref|NR_115207.1| Borrelia afzelii strain VS461 16S ribosomal RNA gene, partial sequence
>gi|636560109|ref|NR_116169.1| Borrelia carolinensis strain SCW-22 16S ribosomal RNA gene, partial sequence
>gi|636559998|ref|NR_116058.1| Borrelia americana strain SCW-41 16S ribosomal RNA gene, partial sequence
>gi|636560106|ref|NR_116166.1| Borrelia americana strain SCW-41 16S ribosomal RNA gene, partial sequence
>gi|265678853|ref|NR_029159.1| Borrelia japonica strain HO14 16S ribosomal RNA gene, partial sequence
>gi|315614511|ref|NR_024713.2| Borrelia sinica strain CMN3 16S ribosomal RNA gene, partial sequence
>gi|559795161|ref|NR_104748.1| Borrelia afzelii strain VS461 16S ribosomal RNA gene, partial sequence
>gi|559795280|ref|NR_104871.1| Borrelia spielmanii strain PC-Eq17N5 16S ribosomal RNA gene, partial sequence
>gi|672239050|ref|NR_125639.1| Borrelia chilensis strain VA1 16S ribosomal RNA gene, partial sequence
>gi|444304237|ref|NR_074662.1| Borrelia afzelii HLJ01 strain HLJ01 16S ribosomal RNA, complete sequence
>gi|444439525|ref|NR_074840.1| Borrelia afzelii PKo strain PKo 16S ribosomal RNA, complete sequence
>gi|444439539|ref|NR_074854.1| Borrelia bavariensis strain PBi 16S ribosomal RNA, complete sequence
>gi|444439550|ref|NR_074865.1| Borrelia duttonii Ly strain Ly 16S ribosomal RNA, complete sequence
>gi|444439551|ref|NR_074866.1| Borrelia recurrentis A1 strain A1 16S ribosomal RNA, complete sequence
>gi|507148149|ref|NR_102956.1| Borrelia bissettii strain DN127 16S ribosomal RNA gene, complete sequence
>gi|507148150|ref|NR_102957.1| Borrelia hermsii DAH strain DAH 16S ribosomal RNA, complete sequence
>gi|507148151|ref|NR_102958.1| Borrelia turicatae 91E135 strain 91E135 16S ribosomal RNA, complete sequence
>gi|507148154|ref|NR_102961.1| Borrelia crocidurae str. Achema strain Achema 16S ribosomal RNA, complete sequence
>gi|526641932|ref|NR_103929.1| Borrelia burgdorferi N40 strain N40 16S ribosomal RNA, complete sequence
>gi|545589139|ref|NR_044732.2| Borrelia burgdorferi strain ATCC 35210 16S ribosomal RNA gene, complete sequence
>gi|659364680|ref|NR_121718.1| Borrelia coriaceae strain Co53 16S ribosomal RNA gene, complete sequence
>gi|659364933|ref|NR_121757.1| Borrelia miyamotoi 16S ribosomal RNA, complete sequence
>gi|659365035|ref|NR_121775.1| Borrelia anserina BA2 strain BA2 16S ribosomal RNA, complete sequence
>gi|659365043|ref|NR_121776.1| Borrelia parkeri 16S ribosomal RNA, complete sequence

No Babesia.

[natasha.sernova]

Dear Agata,

What Babesia are you interested in? Babesia equi, Babesia caballi or another one? Most probably all Babesia have very close or the same sequence of 16S-rRNA, so it doesn't matter...

GCA_000165395.1 PRJNA18731 SAMN02953679 AAXT00000000.1 representative genome 5865 5865 Babesia bovis strain=T2Bo latest Chromosome Major Full 2007/09/06 ASM16539v1 GCF_000165395.1 identical ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000165395.1_ASM16539v1

GCA_000691945.1 PRJEA72411 SAMEA3139016 representative genome 1133968 5868 Babesia microti strain RI strain=RI latest Chromosome Major Full 2012/08/02 ASM69194v1 Universite Montpellier 1 GCF_000691945.1 identical ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000691945.1_ASM69194v1

GCA_000981445.1 PRJEB5046 SAMEA819968 representative genome 5866 5866 Babesia bigemina strain=Bond latest Chromosome Major Full 2014/06/13 Bbig001 SC GCF_000981445.1 identical ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000981445.1_Bbig001

GCA_001077455.1 PRJEB6536 SAMEA2612614 CCSG00000000.1 representative genome 32595 32595 Babesia divergens strain=Rouen 1987 latest Scaffold Major Full 2014/09/06 454hybrid_PBjelly_v2 Spanish National Center for Microbiology na na ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001077455.1_454hybrid_PBjelly_v2

GCA_001650055.1 PRJNA157385 SAMN02203534 JGVA00000000.1 na 5868 5868 Babesia microti strain=ATCC 30222 latest Contig Major Full 2016/05/23 ASM165005v1 IGS na na ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_001650055.1_ASM165005v1

Go inside any genome (ftp-link), here, for example, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000165395.1_ASM16539v1/ open the faa-archieve and search for 16S-rRNA. There are several suspicious *.gz-files, I am not sure which one contains 16S rRNAs... I would look at ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000165395.1_ASM16539v1/ this directory and followed instructions from README.txt - file inside it.

[agata88]

Thank you guys a lot!