Bivalvia TEs

Collection of manually curated LINEs, SINEs and DDE/D-related consensus sequences extracted from bivalve genomes.

Format:

<TE CLASS/SUPERFAMILY>_<SPECIES NAME>_<PROGRESSIVE NUMBER>_cons#<RepeatMasker classification>
e.g: LINE_A.i.concentricus_9_cons#LINE/CR1-Zenon

Consensus sequences construction workflow (LINEs and DDE/D transposons):

1. RepeatMasker annotation of TE using species-specific automatically generated libraries.
2. Extension, Extraction and transaltion of all annotated insertions (min ORF length = 300 aa).
3. Selection of all ORFs with a significant hmmscan hit (e-value < 0.05) against LINE-specific RVT HMM profiles or against DDE/D-related HMM profiles (specific for each DDE/D superfamily, as described in Yuan and Wessler, (2011)).
4. Clustering of all ORF nucleotide sequecens following the 80-80 rule (CD-HIT).
5. Identification of clusters with at least 5 members (for LINEs we also required that at least one sequence posses both RVT and EN domains on the same ORF)
6. Back blastn of each rapresentative sequence against the genome (min 70% identity and coverage), extension and extraction of all hits.
7. Consensus construction using EMBOSS cons (plurality of 3) followed by manual curation and validation.
8. Merging all libraries and reduce redundancy (CD-HIT; 80-80 rule)

Consensus sequences construction workflow (SINEs):

For SINEs elements we selected 12 species for in-depth SINEs annotation using SINE_Scan. SINEs candidates resulting from RepeatModeler and SINE_Scan were merged and subjected to a "Blast-Extend-Extract" process to identify boundaries of the elements and confirm the presence of a 3' tRNA-related head, a conserved domain and a 5' tail.

Accession numbers/sources of genome assemblies:

• Potamilus streckersoni GCA_016746295.1 (NCBI).
• Megalonaias nervosa GCA_016617855.1 (NCBI).
• Solen grandis GCA_021229015.1 (NCBI).
• Sinonovacula constricta GCA_007844125.1 (NCBI).
• Dreissena rostriformis https://phaidra.univie.ac.at/view/o:980132
• Archivesica marissinica GCA_014843695.1 (NCBI).
• Cyclina sinensis GCA_012932295.1 (NCBI).
• Mercenaria mercenaria GCA_014805675.1 (NCBI).
• Ruditapes philippinarum GCA_026571515.1 (NCBI).
• Anadara kagoshimensis GCA_021292105.1 (NCBI).
• Scapharca broughtonii http://dx.doi.org/10.5524/100607
• Tegillarca granosa GCA_013375625.1 (NCBI).
• Myzuhopecten yessoensis GCF_002113885.1 (NCBI).
• Chlamys farreri http://mgbase.qnlm.ac/home
• Pecten maximus GCF_902652985.1 (NCBI).
• Argopecten irradians concentricus https://datadryad.org/stash/dataset/doi:10.5061/dryad.hdr7sqvdr
• Argopecten purpuratus http://mgbase.qnlm.ac/home
• Pinctada fucata http://gigadb.org/dataset/100240
• Saccostrea glomerata http://soft.bioinfo-minzhao.org/srog
• Crassostrea virginica GCF_002022765.2 (NCBI).
• Crassostrea ariakensis GCA_020567875.1 (NCBI).
• Crassostrea gigas GCF_902806645.1 (NCBI).
• Mytilus coruscus GCA_017311375.1 (NCBI).
• Mytilus edulis GCA_019925275.1 (NCBI).
• Limnoperna fortunei http://gigadb.org/dataset/100386
• Modiolus philippinarum https://datadryad.org/stash/dataset/doi:10.5061/dryad.h9942
• Bathymodiolus platifrons https://datadryad.org/stash/dataset/doi:10.5061/dryad.h9942

IMPORTANT The RepeatMasker formatted-style classification for DDE/D and SINEs was automatically generated using RepeatClassifier from the RepeatModeler package and can therefore be innacurate. If you have any correction to suggest please contact jacopo.martelossi2@unibo.it