Molecular Characterization and Gene Expression Profiling ... - CUSAT

2.3.1.6.3. Phylogenetic analysis of the Penaeidin-3
Chapter 2
Phylogenetic tree resulted could be broadly divided into two major
groups. Group I consisting of penaeidins of Litopenaeus, Fenneropenaeus and
Farafantepenaeus sp. and Group II consisting of penaeidins of P. monodon and
F. chineneis (Fig.2.49). The present peptide was found to belong to Group II of
the phylogenetic tree obtained.
2.3.1.7. Penaeidin-5 (GQ334397)
2.3.1.7.1. Nucleotide and deduced amino acid sequences of Penaeidin-5
A partial mRNA transcript of 139 bp, encoding 36 amino acids,
belonging to the penaeidin family of AMPs was obtained from the mRNA of
P. monodon haemocyte by RT-PCR (Fig. 2.50). The sequence was submitted
to GenBank under the accession number GQ334397. The proline rich domain
of the N-terminal region could be seen. Analysis of the putative signal
peptidase cleavage site (SignalP software) indicated a cleavage site located
after position 19 which implied that a penaeidin-5 was a secreted peptide
(Fig. 2.51). Penaeidin signature could be obtained using Motif Scan tool
(Fig.2.52).
2.3.1.7.2. Sequence alignment of Penaeidin-5
BLAST analysis was performed at the nucleotide and amino acid level
with other penaeidin-5 in the GenBank. BLAST analysis showed that the
penaeidin-like AMP shared maximum similarity with penaeidin-5 of P.
monodon, followed by penaeidins of F. chinensis, F. subtilis, F. brasiliensis
(Table 2.14 and 2.15). Multiple alignments showed the presence of highly
conserved sequences at both the nucleotide and amino acid level (Fig.2.53
and 2.54).
2.3.1.7.3. Phylogenetic analysis of the Penaeidin-5
Phylogenetic tree resulted could be broadly divided into three major
groups. Group I consisting of penaeidins of Litopenaeus, Fenneropenaeus,
Penaeus and Farafantepenaeus sp. Group II consisting of penaeidins of P.
Molecular Characterization and Gene Expression Profiling of Antimicrobial Peptides in Penaeid Shrimps
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