README.md

Preliminary analyses for the TETTRIS barcoding project

1) Genomic information

As a first step, I checked NCBI for available Genomic resources for pollinator groups that might become our focus taxonomic groups:

• Syrphidae (hoverflies): COX1; Genomes
• Apoidea (wild bees): COX1; Genomes

The current (21/09/2022) genome lists (also as Excel file) and unprocessed COX-1 FASTA files can be found in the data folder

2) Summary of nuclear gene data available @ BOLD

Here, I used Luise's multifasta dataset and split it by Gene names in multiple files using awk

awk '/^>/ {split($0,a,"|"); gsub("\r", "", a[3]); file=a[3]".fasta"} { print > file }' /media/inter/mkapun/projects/TETTRIS_barcoding/data/BOLD_TestRun/bold_fasta.fas

For each of these multifasta datasets, I then performed multiple alignment in R using the DECIPHER package and calculated Nucleotide Diversity and $\theta$_S (Segregating Sites) using the APE package. The corresponding script can be found here

See the results below:

ID	# samples	SeqLength	NucDiv	$\theta$S
18S	6	530	0.011	0.014
28S	20	685	0.035	0.181
AATS	20	1325	0.103	0.042
CAD	10	558	0.171	0.464
CK1	19	1893	0.059	0.023
COI-3P	20	633	0.110	0.114
COI-5P	20	828	0.104	0.072
PER	17	648	0.148	0.112
RBM15	20	572	0.124	0.215
TULP	17	1201	0.089	0.040