I previously performed this analysis using a different version of our Ostrea lurida genome assembly. Steven asked that I repeat the analysis with a modified version of the genome assembly (Olurida_v081) - only has contigs >1000bp in length.
Genome used: Olurida_v081
I ran RepeatMasker (v4.07) with RepBase-20170127 and RMBlast 2.6.0 four times:
Default settings (i.e. no species select - will use human genome).
Species = Crassostrea gigas (Pacific oyster)
Species = Crassostrea virginica (Eastern oyster)
Species = Ostrea lurida (Olympia oyster)
The idea was to get a sense of how the analyses would differ with species specifications. However, it’s likely that the only species setting that will make any difference will be Run #2 (Crassostrea gigas).
The reason I say this is that RepeatMasker has a built in tool to query which species are available in the RepBase database (e.g.):
<code>RepeatMasker-4.0.7/util/queryRepeatDatabase.pl -species "crassostrea virginica" -stat</code>Here’s a very brief overview of what that yields:
Crassotrea gigas: 792 specific repeats
Crassostrea virginica: 4 Crassostrea virginica specific repeats
Ostrea lurida: 0 Ostrea lurida specific repeats
All runs were performed on roadrunner.
All commands were documented in a Jupyter Notebook (GitHub):
_NOTE: RepeatMasker writes the desired output files (.out, .cat.gz, and *.gff) to the same directory that the genome is located in! If you conduct multiple runs with the same genome in the same directory, it will overwrite those files, as they are named using the genome assembly filename._
RESULTS:
RUN 1 (default settings - human genome)
Output folder:
Summary table (text):
Output table (GFF):
SUMMARY TABLE
<code>
==================================================
file name: Olurida_v081.fa
sequences: 159429
total length: 1140787867 bp (1077373535 bp excl N/X-runs)
GC level: 36.58 %
bases masked: 17954347 bp ( 1.67 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 16599 978030 bp 0.09 %
ALUs 1 292 bp 0.00 %
MIRs 937 72873 bp 0.01 %
LINEs: 3279 752631 bp 0.07 %
LINE1 172 10882 bp 0.00 %
LINE2 646 67827 bp 0.01 %
L3/CR1 659 60327 bp 0.01 %
LTR elements: 569 127808 bp 0.01 %
ERVL 32 1949 bp 0.00 %
ERVL-MaLRs 10 490 bp 0.00 %
ERV_classI 165 17699 bp 0.00 %
ERV_classII 26 1590 bp 0.00 %
DNA elements: 1911 161957 bp 0.02 %
hAT-Charlie 74 4216 bp 0.00 %
TcMar-Tigger 584 24985 bp 0.00 %
Unclassified: 78 9834 bp 0.00 %
Total interspersed repeats: 2030260 bp 0.19 %
Small RNA: 5592 409456 bp 0.04 %
Satellites: 117 21278 bp 0.00 %
Simple repeats: 270784 12935570 bp 1.20 %
Low complexity: 42130 2568284 bp 0.24 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be homo sapiens
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
</code>RUN 2 (species - Crassostrea gigas)
Output folder:
Summary table (text):
Output table (GFF):
SUMMARY TABLE
<code>
file name: Olurida_v081.fa
sequences: 159429
total length: 1140787867 bp (1077373535 bp excl N/X-runs)
GC level: 36.58 %
bases masked: 152816516 bp ( 14.18 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 193250 67253771 bp 6.24 %
SINEs: 2087 284274 bp 0.03 %
Penelope 158576 56080082 bp 5.21 %
LINEs: 179430 61300904 bp 5.69 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 675 348273 bp 0.03 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 7 10781 bp 0.00 %
RTE/Bov-B 7051 1827344 bp 0.17 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 11733 5668593 bp 0.53 %
BEL/Pao 1517 871288 bp 0.08 %
Ty1/Copia 78 72481 bp 0.01 %
Gypsy/DIRS1 9151 4445789 bp 0.41 %
Retroviral 0 0 bp 0.00 %
DNA transposons 233691 33727339 bp 3.13 %
hobo-Activator 17578 1886743 bp 0.18 %
Tc1-IS630-Pogo 39184 6403235 bp 0.59 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 7261 1003937 bp 0.09 %
Tourist/Harbinger 8635 823434 bp 0.08 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 157855 36675484 bp 3.40 %
Total interspersed repeats: 137656594 bp 12.78 %
Small RNA: 222 72690 bp 0.01 %
Satellites: 6260 1238331 bp 0.11 %
Simple repeats: 241081 11662466 bp 1.08 %
Low complexity: 38915 2347827 bp 0.22 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be crassostrea gigas
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
</code>RUN 3 (species - Crassostrea virginica)
Output folder:
Summary table (text):
Output table (GFF):
SUMMARY TABLE
<code>
file name: Olurida_v081.fa
sequences: 159429
total length: 1140787867 bp (1077373535 bp excl N/X-runs)
GC level: 36.58 %
bases masked: 36996910 bp ( 3.43 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 59806 9886111 bp 0.92 %
SINEs: 59806 9886111 bp 0.92 %
Penelope 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 0 0 bp 0.00 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 0 0 bp 0.00 %
RTE/Bov-B 0 0 bp 0.00 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 0 0 bp 0.00 %
Gypsy/DIRS1 0 0 bp 0.00 %
Retroviral 0 0 bp 0.00 %
DNA transposons 8720 2230426 bp 0.21 %
hobo-Activator 0 0 bp 0.00 %
Tc1-IS630-Pogo 0 0 bp 0.00 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 0 0 bp 0.00 %
Tourist/Harbinger 0 0 bp 0.00 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 47005 9434652 bp 0.88 %
Total interspersed repeats: 21551189 bp 2.00 %
Small RNA: 60030 9959172 bp 0.92 %
Satellites: 8 5100 bp 0.00 %
Simple repeats: 259134 12795379 bp 1.19 %
Low complexity: 42184 2581162 bp 0.24 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be crassostrea virginica
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
</code>RUN 4 (species - Ostrea lurida)
Output folder:
Summary table (text):
Output table (GFF):
SUMMARY TABLE
<code>
==================================================
file name: Olurida_v081.fa
sequences: 159429
total length: 1140787867 bp (1077373535 bp excl N/X-runs)
GC level: 36.58 %
bases masked: 15918797 bp ( 1.48 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 0 0 bp 0.00 %
SINEs: 0 0 bp 0.00 %
Penelope 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 0 0 bp 0.00 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 0 0 bp 0.00 %
RTE/Bov-B 0 0 bp 0.00 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 0 0 bp 0.00 %
Gypsy/DIRS1 0 0 bp 0.00 %
Retroviral 0 0 bp 0.00 %
DNA transposons 0 0 bp 0.00 %
hobo-Activator 0 0 bp 0.00 %
Tc1-IS630-Pogo 0 0 bp 0.00 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 0 0 bp 0.00 %
Tourist/Harbinger 0 0 bp 0.00 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 3 189 bp 0.00 %
Total interspersed repeats: 189 bp 0.00 %
Small RNA: 224 73061 bp 0.01 %
Satellites: 8 5100 bp 0.00 %
Simple repeats: 273098 13256460 bp 1.23 %
Low complexity: 42443 2592212 bp 0.24 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be ostrea lurida
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
</code>