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).