Chapter 2 Olsson et al. (2017) scaffolds preparation

The African genome scaffolds from Olsson et al. (2017)…

2.1 Renaming

We renamed scaffolds from Olsson using following code : Olsson_2017_[scaffold name].

scf <- readDNAStringSet(file.path(path, "Olsson_2016", "symph_genome.fa"))
names(scf) <- paste0('Olsson_2017_', names(scf))
dir.create(file.path(path, "Olsson_2016", "db"))
writeXStringSet(scf, file.path(path, "Olsson_2016", "db", "Olsson2017.fa")))

2.2 Removing scaffolds with multimatch blasted consensus sequence from Torroba-Balmori et al. (unpublished)

We will again use the consensus sequence for French Guianan reads from Torroba-Balmori et al. (unpublished), by blasting them on scaffolds from Olsson et al. (2017) with blastn.

cd ~/Documents/BIOGECO/PhD/data/Symphonia_Genomes/Olsson_2016
cd Olsson2017
makeblastdb -in Olsson2017.fa -parse_seqids -dbtype nucl
cd ..
query=~/Documents/BIOGECO/PhD/data/Symphonia_Torroba/assembly/symphoGbS2_outfiles/symphoGbS2.firstline.fasta
blastn -db Olsson2017/Olsson2017.fa -query $query -out blast_consensus_torroba2.txt -evalue 1e-10 -best_hit_score_edge 0.05 -best_hit_overhang 0.25 -outfmt 6 -perc_identity 75 -max_target_seqs 10

blast <- read_tsv(file.path(path, "Olsson_2016", "blast_consensus_torroba2.txt"), col_names = F)
names(blast) <- c("Read", "Scaffold", "Perc_Ident", "Alignment_length", "Mismatches",
                  "Gap_openings", "R_start", "R_end", "S_start", "S_end", "E", "Bits")
write_file(paste(unique(blast$Scaffold), collapse = "\n"), 
           file.path(path, "Olsson_2016", "selected_scaffolds_blast_consensus2.list"))

seqtk subseq Olsson2017/Olsson2017.fa selected_scaffolds_blast_consensus2.list >> selected_scaffolds_blast_consensus2.fa

We finally have most of scaffolds with on match in a broad range of sizes (from 100 bp to 33.2 kbp). In total 688 scaffolds from Olsson et al. (2017) match consensus sequences from Torroba-Balmori et al. (unpublished). But several scaffolds obtained multiple matches that we cannot use for probes. We will thus exclude the whole scaffold if the scaffold is shorter than 2000 bp or the scaffold region matching the raw read if the scaffold is longer than 2000 bp.

Figure 2.1: Number of match with Torroba consensus reads vs gene width.

Table 2.1: Scaffold to cut due to multiple read match.

Scaffold	width	remove	cut
Olsson_2017_deg7180004393135	2380		1700-1631
Olsson_2017_deg7180004374686	2120		2073-1992
Olsson_2017_scf7180005372912	3152		3102-3152
Olsson_2017_scf7180005387046	2048		174-256
Olsson_2017_scf7180005323991	2482		2330-2267

Following scaffolds will be removed due to multitple matches and a length \(<200bp\): deg7180004378417, deg7180003744575, deg7180002657883, deg7180004705895, deg7180004369764, deg7180002776754, deg7180004453462, deg7180004453461, deg7180002668453, deg7180005298947, deg7180003723902, deg7180005298948, deg7180004372504, deg7180002659849, deg7180004372505, deg7180004377385, deg7180003260802, deg7180003625436, deg7180004705895, deg7180002776754, deg7180004705894, deg7180002852093, deg7180004822905, deg7180005023024, deg7180004478675, deg7180004428004, deg7180004428003, deg7180004507379, deg7180002656221, deg7180004374687, deg7180004372498, deg7180004372497, deg7180002654368, deg7180002674357, deg7180004700334, deg7180004899808, deg7180004899808, deg7180002726303, scf7180005372913, deg7180005163225, deg7180003214542, scf7180005400822, deg7180005163224, deg7180003138164, deg7180004981997, deg7180004981996, deg7180005171251, deg7180005106503, deg7180003910181, deg7180005026532, deg7180003853280, deg7180004724986, deg7180005246885, deg7180004710959, deg7180004681149, deg7180004580422, deg7180004472718, deg7180003290510, deg7180005004768, deg7180004756559, scf7180005435685, deg7180004725719, deg7180004599019, deg7180004599018, deg7180002749392, deg7180002739372, deg7180004754314, deg7180004847375, deg7180004580009, deg7180004386399, deg7180004377195, deg7180004377194, deg7180004399409, deg7180004392029, deg7180004385805, deg7180004386398, deg7180002816623, deg7180002985310, scf7180005421751, deg7180004374725, deg7180004372798, deg7180004374726, deg7180002668107, deg7180003199928, deg7180003093903, deg7180003310549, deg7180004796671, deg7180003505925, deg7180002988969. And other will be cut (see table 2.1).

2.3 Total filtered scaffolds

References

Olsson, S., Seoane-Zonjic, P., Bautista, R., Claros, M.G., González-Martínez, S.C., Scotti, I., Scotti-Saintagne, C., Hardy, O.J. & Heuertz, M. (2017). Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers. Molecular Ecology Resources, 17, 614–630. Retrieved from http://doi.wiley.com/10.1111/1755-0998.12605