Biology Reference
In-Depth Information
DQB
Fourteen unique sequences were detected in this study, and they were labeled from
Neph-
DQB*01
to
Neph-DQB*14
(GenBank accession nos. DQ843614-DQ843623 and EF056477-
EF056480). Five of these sequences, i.e.
Neph-DQB*06
, 0
7
, 0
8
, 0
9
and
10
, have previously
been reported from porpoises in Japanese waters (Hayashi et al.
2003). In the 14 sequences,
five were found to be population-specific, i.e.
Neph-DQB*02, Neph-DQB*13
and
Neph-
DQB*11
,
12
,
14
appeared in the South China Sea population, Yellow Sea population, and
Yangtze River population, respectively, whereas the remaining nine sequences were shared
by population pairs. None of the sequences contained insertions/deletions (or indels), or stop
codons, suggesting that all sequences might come from functional molecules in the genome.
More than two
DQB
sequences were detected in 8 out the 195 individuals examined in this
study. Five of the eight porpoises had three unique sequences, two of them had four, and the
last one had five, suggesting at least three copies of the
DQB
gene existed in finless
porpoises. Compared with
Neph-DRA
,
DQB
had a relatively higher variability of 12.8%
(22/172) at the nucleotide level and 24.6% (14/57) at the amino acid level (Figure 1b). The
number of pairwise nucleotide differences between pairs of sequences ranged from 1 (
Neph-
DQB
*
01
vs.
Neph-DQB
*
02
) to 16 (
Neph-DQB
*
10
vs.
Neph-DQB
*
14
), and the number for
amino acid varied from 0 (
Neph-DQB
*
06
vs.
Neph-DQB
*
11
) to 11 (
Neph-DQB
*
10
vs.
Neph-
DQB
*
14
). These values indicate the divergence both within and between loci as we were not
able to distinguish unique sequences of particular loci according to gene trees. But in further
analyses, we considered all sequences as if they would be alleles of one locus. In addition, the
rate of nonsynonymous substitutions was more than four times higher than that of
synonymous substitutions (
P
= 0.071,
Z
-test of positive selection) in the putative PBR, while
the rate decreased to two (
P
= 0.148,
Z
-test of positive selection) in the Non-PBR (Table 2).
MHC-I
Thirty-four unique sequences were identified for the MHC-I gene (GenBank accession
nos. DQ843624-DQ843657). No indels or stop codons were detected. However, these
sequences are possibly active members of three loci rather than a single specific locus
because three to five distinct sequences were detected from most of the individuals. In
addition, it is very difficult to divide loci on a genetic tree and we considered all sequences as
if they would be alleles of one locus in the following analyses. The variability was 47 of 147
(32.0%) in nucleotide sequences and 25 of 49 (51.0%) in amino acid residues (Figure 1c).
Nucleotide sequence variation between all pairwise comparisons of
Neph-I
sequences ranged
from 1 (
Neph-I
*
02
vs.
Neph-I
*
26
) to 25 nucleotides (
Neph-I
*
14
vs.
Neph-I
*
26
), whereas
amino acid substitutions ranged from 1 (
Neph-I
*
02
vs.
Neph-I
*
26
) to 19 (
Neph-I
*
14
vs.
Neph-I
*
22
). The detected number of unique sequences was 13 for 134 clones from 22
Yangtze samples, 22 for 100 clones from 20 Yellow Sea samples, and 26 for 133 clones from
26 South China Sea samples, respectively. The five common sequences of
Neph-I*01
,
02
,
03
,
04
and
I*07
were the most frequent and widespread in the three populations, and 17
sequences were shared only by some population pairs. In addition, 12 population-specific
sequences were identified, four (
I*06
,
I*14
,
I*23
,
I*32
) in the Yangtze River population, five
(
I*21
,
I*24
,
I*25
,
I*31
,
I*34
) in the South China Sea population, and three (
I*12
,
I*26
,
I*27
)
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