Table 1. DNA profiles of pearl samples from Pinctada margaritifera (PMR), P. maxima (PMX) and P. radiata (PR) based on four different molecular markers.
| Pearl sample | Pearl weight (carats/mg) | Sample weight (mg) | 16S rRNA | cox1 | ITS1 rRNA | ITS2 rRNA |
| PMR positive control | PMR (AB214436.1)a | PMR (AB259166.1) | PMR (AY877501.1) | PMR (AY877506.1) | ||
| 511 bp (99%)b | 575 bp (99%) | 675 bp (99%) | 575 bp (100%) | |||
| PMX positive control | PMX (AB214435.1) | PMX (GQ452847.1) | PMX (AY172345.1) | PMX (AY877505.1) | ||
| 509 bp (100%) | 476 bp (99%) | 593 bp (99%) | 571 bp (100%) | |||
| PR positive control | PR (AB214442.1) | PR (GQ355875.1) | P. martensii c (AY172344.1) | P. fucata c (AY877582.1) | ||
| 524 bp (100%) | 575 bp (99%) | 580 bp (99%) | 591 bp (99%) | |||
| PMR1 | 11.1/2228 | 426 | PMR (AB214436.1) | PMR (AF374329.1) | PMR (AY877501.1) | PMR (AY877506.1) |
| 511 bp (99%) | 425 bp (99%) | 675 bp (99%) | 575 bp (100%) | |||
| PMR2 | 8.1/1610 | 19 | PMR (AB214436.1) | PMR (AF374329.1) | PMR (AY877501.1) | PMR (AY877506.1) |
| 455 bp (99%) | 425 bp (99%) | 378 bp (100%) | 575 bp (100%) | |||
| PMR3 | 7.4/1480 | 24 | n.d.d | n.d. | n.d. | PMR (AY877506.1) |
| 575 bp (100%) | ||||||
| PMR4 | 7.4/1480 | 124 | PMR (AB214436.1) | PMR (AF374329.1) | PMR (AY877501.1) | PMR (AY877506.1) |
| 455 bp (99%) | 425 bp (99%) | 378 bp (100%) | 575 bp (100%) | |||
| PMR5 | 13.1/2618 | 318 | PMR (AB214436.1) | PMR (AF374329.1) | n.d. | PMR (AY877506.1) |
| 455 bp (100%) | 425 bp (99%) | 575 bp (100%) | ||||
| PMR6 | 9.8/1964 | 23 | PMR (AB214436.1) | PMR (AF374326.1) | n.d. | PMR (AY877506.1) |
| 454 bp (99%) | 425 bp (100%) | 575 bp (100%) | ||||
| PMX1 | 33.0/6598 | 78 | PMX (AB214435.1) | n.d. | n.d. | PMXe |
| 451 bp (100%) | ||||||
| PMX2 | 29.5/5898 | 135 | PMX (AB214435.1) | n.d. | n.d. | PMX (AY883851.1) |
| 451 bp (100%) | 571 bp (100%) | |||||
| PMX3 | 20.9/4180 | 34 | PMX (AB214435.1) | PMX (GQ452847.1) | n.d. | PMX (AY282737.1) |
| 451 bp (100%) | 204 bp (100%) | 571 bp (100%) | ||||
| PMX4 | 25.3/5070 | 105 | PMR (AB214436.1) | n.d | n.d. | PMR (AY877506.1) |
| 454 bp (99%) | 575 bp (99%) | |||||
| PMX5 | 13.5/2694 | 38 | n.d. | n.d. | n.d. | n.d. |
| PMX6 | 8.4/1672 | 59 | n.d. | n.d. | n.d. | n.d. |
| PR1 | 6.2/1234 | 108 | PR (AB214442.1) | n.d. | P. martensii (AY144602.1) | P. fucata (AY877582.1) |
| 444 bp (100%) | 226 bp (99%) | 590 bp (99%) | ||||
| PR2 | 5.4/1090 | 79 | PR (AB214442.1) | PR (GQ355875.1) | P. martensii (AY144602.1) | P. fucata (AY877588.1/AY877600.1)f |
| 444 bp (100%) | 543 bp (99%) | 226 bp (99%) | 221 bp/239 bp (100%) | |||
| PR3 | 5.1/1030 | 296 | PR (AB214442.1) | n.d. | n.d. | P. fucata (AY877582.1) |
| 523 bp (100%) | 491 bp (99%) | |||||
| PR4 | 4.5/908 | 224 | PR (AB214442.1) | PR (GQ355875.1) | P. martensii e | P. fucata (AY877588.1/AY877600.1)f |
| 523 bp (100%) | 543 bp (99%) | 221 bp/239 bp (100%) | ||||
| PR5 | 4.5/904 | 151 | n.d. | P. fucata (DQ299941.1) | n.d. | P. fucata (AY877582.1) |
| 149 bp (91%) | 491 bp (99%) | |||||
| PR6 | 4.2/842 | 83 | PR (AB214442.1) | PR (GQ355875.1) | n.d. | P. fucata (AY877605.1) |
| 523 bp (100%) | 543 bp (99%) | 242 bp (99%) |
a
Pinctada species assignment was based on the highest BLAST score (highest query coverage and maximal base pair identity). GenBank accession number shown in brackets.
b
amplicon size (base pair) and maximal identity (%) of the sequence to the BLAST query.
c
P. fucata and P. martensii are conspecific to P. radiata on the basis of their ITS sequences [50], [51].
d
not determined.
e
sample had lower sequence quality, but the BLAST query in GenBank indicated the correct Pinctada species. The ITS2 sequences could be amplified and successfully analyzed using PCR-RFLP.
f
these two accession numbers correspond to ITS2 sequences which flanked an internal sequence of ∼30 bp characterized by double peaks consistent with heterozygosity.