Molecular Characterization and Gene Expression Profiling ... - CUSAT

Chapter 2
chinensis and F. indicus (Table 2.10 and 2.11). Sequence alignments at the
nucleotide and amino acid levels showed the presence of highly conserved
sequences within the crustin molecule (Fig 2.41 and 2.42)
2.3.1.5.5. Phylogenetic analysis of Crustin-3
The bootstrap distance tree calculated for the resulting crustin
sequences of shrimps could be grouped into four major groups (Fig.2.43).
Group I consisted of crustins of Litopenaeus, Fenneropenaeus and
Farfantepenaeus sp. Group II consisted of crustin isoforms of M. japonicus,
Group III of P. monodon, and Group IV of F. chinensis. Phylogenetic analysis
of crustins of all decapods could be broadly divided into two groups. Group
I consisting of shrimp crustins and Group II consisting of crustins of crabs,
crayfishes and lobsters (Fig.2.44).
2.3.1.6. Penaeidin-3 (GU732819)
2.3.1.6.1. Nucleotide and deduced amino acid sequences of Penaeidin-3
A partial mRNA transcript of 138 bp, encoding 45 amino acids,
belonging to the penaeidin family of AMPs was obtained from the mRNA of
P. monodon haemocyte by RT-PCR (Fig. 2.45). The sequence was submitted
to GenBank under the accession number GU732819. Four cysteine residues
could be found in the partial sequence that form the part of the six cysteine
residues organized in two doublets. Penaeidin signature could be detected
within the sequence using Motif Scan tool (Fig.2.46).
2.3.1.6.2. Sequence alignment of Penaeidin-3
BLAST analysis was performed at the nucleotide and amino acid level
with other penaeidin-3 in the GenBank. BLAST analysis showed that the
penaeidin-like AMP shared maximum similarity with penaeidin-3 of P.
monodon (Table 2.12 and 2.13). Multiple alignment performed for the
sequence showed the presence of highly conserved sequences both at the
nucleotide and amino acid level (Fig.2.47 and 2.48).
Molecular Characterization and Gene Expression Profiling of Antimicrobial Peptides in Penaeid Shrimps
130