Roseibaca
Roseibaca
Intro
In this repository, we conduct a study of Roseibaca V10, a strain belonging to the Rhodobacteraceae family, focusing on its evolution from a biosynthetic perspective. The family used for this study can be seen in the file list.txt and is given by:
| Assembly accesion | Organims | Strain |
|---|---|---|
| GCF_023336755.1 | Roseibaca sp.V10 | V10 |
| GCF_001517585.1 | Roseibaca calidilacus | HL-91 |
| GCF_900499075.1 | Roseibaca ekhonensis | CECT 7235 |
| GCF_001870675.1 | Roseinatronobacter thiooxidans | ALG1 |
| GCF_006716865.1 | Roseinatronobacter monicus | DSM 18423 |
| GCF_004366635.1 | Rhodobaca bogoriensis | DSM 18756 |
| GCF_001870665.2 | Rhodobaca barguzinensis | alga05 |
| GCF_014681765.1 | Roseicitreum antarcticum | ZS2-28 |
| GCF_003076755.1 | Pararhodobacter oceanensis | AM505 |
| GCF_003990445.1 | Pararhodobacter zhoushanensis | ZQ420 |
| GCF_003122215.1 | Pararhodobacter marinus | CIC4N-9 |
| GCF_003075525.1 | Pararhodobacter aggregans | D1-19 |
| GCF_016653255.1 | Rhodobaculum claviforme | LMG 28126 |
| GCF_003350345.1 | Alkalilacustris brevis | 34079 |
| GCF_000740775.1 | Haematobacter missouriensis | CCUG 52307 |
| GCF_003254295.1 | Rhodobacter capsulatus | DSM 1710 |
| GCF_000740785.1 | Paenirhodobacter enshiensis | DW2-9 |
| GCF_000714535.1 | Thioclava pacifica | DSM 10166 |
| GCF_003034995.1 | Phaeovulum veldkampii | DSM 11550 |
| GCF_900100045.1 | Paracoccus denitrificans | DSM 413 |
| GCF_009908165.1 | Frigidibacter albus | SP32 |
| GCF_002927635.1 | Albidovulum inexpectatum | DSM 12048 |
| GCF_003034965.1 | Fuscovulum blasticum | DSM 2131 |
| GCF_003290025.1 | Pseudogemmobacter bohemicus | Cd-10 |
| GCF_002900975.1 | Tabrizicola aquatica | RCRI19 |
| GCF_001294535.1 | Cypionkella psychrotolerans | PAMC 27389 |
| GCF_900110025.1 | Gemmobacter aquatilis | DSM 3857 |
| GCF_000420745.1 | Pseudorhodobacter ferrugineus | DSM 5888 |
| GCF_003034985.1 | Cereibacter changlensis | JA139 |
| GCF_004015795.1 | Falsirhodobacter deserti | W402 |
| GCF_000429765.1 | Gemmobacter nectariphilus | DSM 15620 |
| GCF_002871005.1 | Acidimangrovimonas sediminis | MS2-2 |
| GCF_004010155.1 | Solirhodobacter olei | Pet-1 |
| GCF_020667835.1 | Roseibaca sp.Y0-43 | Y0-43 |
| GCF_013415485.1 | Rhabdonatronobacter sediminivivens | IM2376 |
| GCF_001884735.1 | Natronohydrobacter thiooxidans | AH01 |
| GCF_028745735.1 | Roseinatronobacter sp.HJB301 | HJB301 |
Data Preparation
Download Genomes
The .fna files for each of the strains were downloaded from NCBI using the ncbi-genome-download conda environment and were stored in the raw_data.
Functional Annotation
Functional annotation was performed with Prokka 1.14.6, and the details for each strain can be found in functional_annotation.
Genbank
This folder contains the .gbk files that resulted from the functional annotation performed with Prokka. These files were corrected using the following script, correctgbk.sh, which allows us to replace the term “Unclassified” in the “Organism” field with the respective strain for each organism.
file=$1
locus=$(grep -m 1 "DEFINITION" $file |cut -d " " -f6,7) #if you have details the strain in your gbk files, use this line. Else use the next line.
#locus=$(grep -m 1 "LOCUS" $file |cut -d\ -f 8 |cut -b1-11) #select the first 11 characters from the first "LOCUS"
perl -p -i -e 's/\n// if /ORGANISM/' $file #cambiar
perl -p -i -e 's/\s*Unclassified/ '"${locus}"'/' $file
Additionally, we rename the files to include the details of each organism.
cat list.txt | while read line
do
id2=$(echo $line |cut -d " " -f1,2,3,4,5 | tr " \t" "_")
id=$(echo $line |cut -d " " -f1)
#echo $id.prokka
#echo $id2
mv $id.prokka.gbk $id2.gbk
done
Biosynthetic Gene Cluster (BGC) Clustering
We used antiSMASH 7.0.0 to search for BGCs, and the results were stored in the antismash7 folder. Additionally, we used the change-names.sh script, which adds the strain details to each of the regions found by antiSMASH.
We found 6 BGCs for Roseibaca V10, as can be seen in the output of antismash. The relationship of these clusters with other clusters in different genomes still needs to be investigated.
BGC Similarity Networks
To identify the groups of BGCs that are forming and to determine in which groups Roseibaca sp.V10 is present, we used BiG-SCAPE 1.1.2. The results can be found in the bigscpae_nuevos/output_3107 folder.
A graphical exploration of the BiG-SCAPE results can be seen at bigscpae_nuevos/output_3107/index.html.
Terpene
We have the following table showing the presence and absence of genomes containing the BGC that produces Terpene.
In this table, we can observe the family FAM_00146, which includes our target genome Roseibaca_sp.V10.
FAM_00146
- GCF_001517585.1_Roseibaca_calidilacus_HL-91-NZ_FBYC01000004.1.region001
- GCF_023336755.1_Roseibaca_sp.V10_V10-NZ_JALZWP010000001.1.region001
- GCF_900499075.1_Roseibaca_ekhonensis_CECT_7235-NZ_UIHC01000012.1.region001
- GCF_020667835.1_Roseibaca_sp.Y0-43_Y0-43-NZ_JAFMPR010000008.1.region001
RiPPs
We have the following table showing the presence and absence of genomes containing the BGC that produces *RiPPs.*
In this table, we can observe the family FAM_00120, which includes our target genome Roseibaca_sp.V10.
FAM_00120
- GCF_023336755.1_Roseibaca_sp.V10_V10-c00009_NZ_JALZ…region001
- GCF_900499075.1_Roseibaca_ekhonensis_CECT_7235-NZ_UIHC01000019.region001
PKSother
We have the following table showing the presence and absence of genomes containing the BGC that produces Other.
we can observe the family FAM_00117, which includes our target genome Roseibaca_sp.V10.
FAM_00117
- GCF_023336755.1_Roseibaca_sp.V10_V10-NZ_JALZWP010000002.1.region001
- GCF_900499075.1_Roseibaca_ekhonensis_CECT_7235-NZ_UIHC01000006.1.region001
PKS -NRP Hybrids
We have the following table showing the presence and absence of genomes containing the BGC that produces Other.
we can observe the family FAM_00135, which includes our target genome Roseibaca_sp.V10.
FAM_00135
- GCF_001517585.1_Roseibaca_calidilacus_HL-91-NZ_FBYC01000004.1.region003
- GCF_023336755.1_Roseibaca_sp.V10_V10-NZ_JALZWP010000002.1.region002
- GCF_900499075.1_Roseibaca_ekhonensis_CECT_7235-NZ_UIHC01000007.1.region001
Others
We have the following table showing the presence and absence of genomes containing the BGC that produces Other.
we can observe the family FAM_00119, which includes our target genome Roseibaca_sp.V10.
FAM_00135
- GCF_001517585.1_Roseibaca_calidilacus_HL-91-NZ_FBYC01000004.1.region002
- GCF_023336755.1_Roseibaca_sp.V10_V10-NZ_JALZWP010000003.1.region001
- GCF_900499075.1_Roseibaca_ekhonensis_CECT_7235-NZ_UIHC01000001.1.region001
- GCF_020667835.1_Roseibaca_sp.Y0-43_Y0-43-NZ_JAFMPR010000001.1.region001
CORASON
CORASON (Clustering ORthologous proteins in Antibiotic Synthesis) is a tool specifically designed for the exploration and analysis of biosynthetic gene clusters. It allows the comparison of gene clusters across different genomes and facilitates the identification of conserved gene sets, which can provide insights into the functional and evolutionary relationships of these clusters.
By using CORASON, we aimed to identify common core genes or gene neighborhoods shared between Roseibaca sp.V10 and other genomes, which could indicate potential similarities in the biosynthetic capabilities or pathways. This analysis would provide a broader context for understanding the functional characteristics of Roseibaca sp.V10’s biosynthetic potential.
The output and results of the CORASON analysis can be found in the corresponding folder corason/svg/new/ . The analysis may reveal clusters with similar core genes or shared gene neighborhoods, shedding light on the relationships and potential similarities between Roseibaca sp.V10 and other genomes in terms of biosynthetic capabilities.
Ectoine
For ectoine, we used the gene BMJDCPAI_00849 as the query, and here are the results:
The CORASON analysis with the gene BMJDCPAI_00849 as the query identified several clusters in different genomes that share similarity with the ectoine biosynthetic pathway. These clusters may contain genes involved in the synthesis of ectoine or related compounds.
The analysis revealed the following clusters:
Cluster 1: GCF_001517585.1_Roseibaca_calidilacus_HL-91-NZ_FBYC01000004.region001
Genes involved in ectoine biosynthesis: BMJDCPAI_00849, BMJDCPAI_00850, BMJDCPAI_00851, BMJDCPAI_00852, BMJDCPAI_00853 Cluster 2: GCF_023336755.1_Roseibaca_sp.V10_V10-c00001_NZ_JALZ…region001
Genes involved in ectoine biosynthesis: BMJDCPAI_00849, BMJDCPAI_00850, BMJDCPAI_00851, BMJDCPAI_00852, BMJDCPAI_00853 Cluster 3: GCF_900499075.1_Roseibaca_ekhonensis_CECT_7235-NZ_UIHC01000012.region001
Genes involved in ectoine biosynthesis: BMJDCPAI_00849, BMJDCPAI_00850, BMJDCPAI_00851, BMJDCPAI_00852, BMJDCPAI_00853 These clusters indicate the presence of a conserved set of genes associated with ectoine biosynthesis in the genomes mentioned above. The shared presence of these genes suggests that these organisms may have the capability to produce ectoine or similar compounds.
RRE
In addition, using RRE (Rapid Response Engine), we analyzed the gene BMJDCPAI_02120 as the target gene and identified a gene family that includes Roseibaca_v10.
The analysis with BMJDCPAI_02120 revealed a gene family that is shared with Roseibaca_ekhonensis. This gene family may be associated with a specific biological function or metabolic pathway.
Further details and a comprehensive analysis of the gene family can be found in the RRE output files.
T3PKS
Additionally, we performed an analysis using T3pks (Type III Polyketide Synthase) with the query gene BMJDCPAI_00537. The results show the presence of a T3pks gene family that includes Roseibaca_ekhonensis.
Further examination of the T3pks gene family and its associated metabolic pathways can be explored in the output files generated from the analysis.
Terpene
In the Terpene analysis using the query gene BMJDCPAI_00103., we identified a gene family associated with Terpene biosynthesis. This gene family includes Roseibaca_ekhonensis, indicating the potential involvement of this organism in Terpene production.
The presence of the Terpene biosynthetic gene in Roseibaca_ekhonensis suggests its capability to produce Terpene compounds. Further investigation into the specific Terpene biosynthetic pathways and the functional characteristics of the gene family can be explored using the output files generated from the analysis.
NRPST1PKS
In the analysis using the NRPST1PKS query gene BMJDCPAI_00764 , we identified a gene family associated with nonribosomal peptide synthetase (NRP) and type I polyketide synthase (PKS) biosynthesis. Although Roseibaca_ekhonensis was part of this gene family, it’s important to note that our main focus is Roseibaca V10.
To investigate the presence of NRPST1PKS biosynthetic gene clusters in Roseibaca V10, we can perform a specific analysis using the corresponding gene sequence from Roseibaca V10 as the query. This analysis will provide more accurate information about the potential biosynthetic capabilities of Roseibaca V10 in producing nonribosomal peptides and type I polyketides.
T1PKS
To investigate the presence of T1PKS biosynthetic gene clusters in Roseibaca V10, we can perform a specific analysis using the corresponding gene sequence from Roseibaca V10 as the query. This analysis will provide more accurate information about the potential biosynthetic capabilities of Roseibaca V10 in producing type I polyketides.
We use this query BMJDCPAI_03118
And other query BMJDCPAI_03119
