of 19
Supplementary Figures
- Molecular evolutionary trends and biosynthe
sis
pathways in the
Oribatida revealed by the genome of
Archegozetes longisetosus
Adrian Brückner
, Austen A. Barnett
, Prashant Bhat
, Igor A. Antoshechkin
and Sheila A. Kitchen
Figure S1
Results of
in silico
genome size estimations based on jellyfish
k
-mer
counting using
a:
GenomeScope v1.0 and
b
and
c
: the findGSE v0.1.0 R package
(Sun
et al.
, 2018)
.
Figure S2
P
hylogenetic placement of
Archegozetes longisetosus
among other chelicerates.
a
:
Maximum likelihood phylogeny based on concatenation of 1,121
orthologs
Branch lengths unit is
substitutions per site
and
the node values reflect bootstrap supports.
b
: Coalescence species tree
reconstruction of the 1,121 filtered orthogroups. Branch lengths are presented in coalescent units
(differences in the 1,121 gene trees) and the node values reflect the local posterior probabilities.
Figure S3
C
omparisons of protein-
coding genes of 23 arthropod species, including
Archegozetes
.
The bar charts show th
e proportion of orthrogroup conservation with each species (see insert
legend) based on OrthoFinder clustering.
Figure S4
Maximum likelihood phylogenetic analyses of the
A. longisetosus
Paired protein
orthologs.
(a)
Maximum likelihood tree showing the rel
ationship of the Eyegone, Pax-
3/7, and
Pax
-6 clades as collapsed subtrees.
(b)
The un-
collapsed clade in
A
showing the phylogenetic
relationships of selected Eyegone proteins and the putative
A. longisetosus
Eyegone ortholog.
(c)
The un-
collapsed clade in
A
showing the phylogenetic relationships of selected Pax-
3/7 proteins
and the putative
A. longisetosus
Pax
-3/7 orthologs.
(d)
The un-
collapsed clade in
A
showing the
phylogenetic relationships of selected Pax-
6 proteins and the putative
A. longisetosus
Pax
-6
ortholog. All
A. longisetosus
orthologs are in red, and the
D. melanogaster
orthologs are in blue.
Node support was calculated using the approximate likelihood ratio (aLRT) method and is
represented by the color of each node. All taxa are represented by their species names, gene names
if given, and their NCBI accession numbers.
(a)