2.7 Identification of gene family members
To understand the mechanisms of benthic adaptation and metamorphosis in
Chironomidae, the key gene families associated with in the genomes ofC. striatipennis , C. riparius , C. tentans , C.
marinus , P. vanderplanki and P. akamus i were analyzed.
To identify Globin genes, all of 347 Globin sequences of Chironomidae
were downloaded from NCBI Genbank and then BLASTP was used to search
Homologous protein gene sequences (Kent, 2002). The Globin hmmer from
Pfam (http://pfam.xfam.org) was employed to train new species
Hidden Markov Model (HMM) by HMMER 3.0 (http://www.hmmer.org/) and
search for genome (Jiang et al., 2008). The common genes were combined
to obtain the putative gene families which were searched from the Pfam
to confirm that it contained NBS conserved domain.
To identify CYP450s genes and GSTs genes, the GSTs sequences and the
CYP450 reference protein sequences were downloaded from NCBI Genbank,
respectively, and then BLASTP was used to search Homologous protein gene
sequences (Kent, 2002). The GSTs homologous gene sequence and the P450
hmmer from Pfam (http://pfam.xfam.org) were used to train new
species Hidden Markov Model (HMM) by HMMER 3.0
(http://www.hmmer.org/) and search for genome, respectively (Jiang
et al., 2008). The common genes were combined to obtain the putative
gene families which were searched from the Pfam to confirm that it
contained NBS conserved domain.
To identify JHAMT(juvenile hormone acid methyl transferase)genes and
CASP7 genes,all of the JHAMT sequences and the CASP 7 sequences ofDrosophila were downloaded from NCBI Genbank, and then BLASTP was
used to search Homologous protein gene sequences, respectively (Kent,
2002). The Homologous protein gene sequences were used to train the
JHAMT hmm model and CASP7 hmm model, respectively. The newly trained hmm
model was used to search their gene sequences (Jiang et al., 2008).
Finally, we combined the common genes as the putative gene families.
The protein sequences of each gene families were aligned by Muscle
v3.8.1551 and phylogenetic tree was constructed by IQTREE with default
parameters (Katoh & Standley, 2013). The phylogenetic tree was
visualized using EvolView v3
(https://www.evolgenius.info/)
(Subramanian et al., 2019).