Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling and DNA Extraction
2.2. PCR Amplification, Cloning and Sequencing
2.3. Sequence Analysis
3. Results
3.1. Complete nrDNA Sequences of R. philippinarum and M. mercenaria
3.2. Informative Characteristics of the IGS Region
3.3. Phylogenetic Analysis of Veneridae Based on ITS and 18S rRNA Sequence
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Subfamily | Genus | Species | ITS | 18S | 28S | |||
---|---|---|---|---|---|---|---|---|
GenBank Accession Number | Length (bp) | GenBank Accession Number | Length (bp) | GenBank Accession Number | Length (bp) | |||
Meretricinae | Meretrix | Meretrix lusoria | DQ389108 | 1567 | JN996714 | 1899 | MW221234 | 739 |
Meretricinae | Meretrix | Meretrix meretrix | AY695801 | 1480 | EF426291 | 1900 | / | / |
Tapetinae | Ruditapes | Ruditapes philippinarum | DQ399404 | 1303 | JN807343 | 1833 | AM779742 | 1476 |
Tapetinae | Ruditapes | Ruditapes variegatus | JN807381 | 1265 | JN807349 | 1832 | DQ343858 | 1388 |
Tapetinae | Ruditapes | Ruditapes decussatus | HQ634139 | 1259 | KX713340 | 1779 | KX713427 | 2078 |
Tapetinae | Paratapes | Paphia undulata | EU183531 | 1236 | JN996722 | 1831 | JQ277802 | 743 |
Chioninae | Leukoma | Protothaca staminea | EF035084 | 1379 | AM774570 | 1779 | AM779744 | 1478 |
Chioninae | Leukoma | Protothaca jedoensis | DQ220291 | 1437 | EF426292 | 1831 | DQ343856 | 1390 |
Chioninae | Mercenaria | Mercenaria mercenaria | DQ190445 | 1332 | AF106073 | 1804 | KX713401 | 2085 |
Callistinae | Saxidomus | Saxidomus gigantea | EF035110 | 1332 | / | / | / | |
Cyclininae | Cyclina | Cyclina sinensis | DQ190446 | 1263 | EF426289 | 1838 | DQ343849 | 1396 |
outgroup | Perna viridis | MH279802 | 735 | KY081342 | 1698 | MK419106 | 3679 |
Amplified Region | Primers | Sequences (5′–3′) | Annealing Temperature | Extension Time | Length (bp) |
---|---|---|---|---|---|
18S rRNA | 18S-ar | TCAAATGTCTGCCCTATC | 53 °C for R. philippinarum, 55 °C for M. mercenaria | 1 min 30 s | 1501–1573 |
18S-br | TTCACCTACGGATACCTTG | ||||
18S rRNA–ITS-28S rRNA | ITS-ar | TAACAAGGTATCCGTAGGTG | 53 °C for R. philippinarum, 55 °C for M. mercenaria | 1 min | 1436–1841 |
ITS-br | CGTGCCAGTATTTAGCC | ||||
28S rRNA | 28S1-ar | AGTCGGGTTGTTTGGGAATG | 55 °C | 1 min | 1240–1251 |
28S1-br | TTGATTCGGCAGGTGAGTTG | ||||
28S2-ar | CTGTGGGATGAACCAAACGC | 55 °C | 1 min 30 s | 1649–1691 | |
28S2-br | ACCTTAGGACACCTGCGTTA | ||||
28S3-ar | TCACCCACTAATAGGGAACG | 55 °C | 1 min | 691–702 | |
28S3-br | AAGCACCTAAACCAAATGTC | ||||
IGS for R. philippinarum | IGS-ar1 | CCAAATGCCTCGTCATCTAA | 59 °C | 6 min 30 s | 7829 |
IGS-br1 | CTGCCTTCCTTGGATGTG | ||||
IGS for M. mercenaria | IGS-ar2 | GAATACAGACCGTGAAAGCG | 56 °C | 5 min 30 s | 6434 |
IGS-br1 | CTGCCTTCCTTGGATGTG |
Region | Ruditapes philippinarum | Mercenaria mercenaria | Alignment Length (bp) | Pairwise Identity (%) | Pairwise Distance | Variable Site (V) | ||
---|---|---|---|---|---|---|---|---|
Length (bp) | GC Content (%) | Length (bp) | GC Content (%) | |||||
18S rRNA | 1832 | 51.85 | 1830 | 51.75 | 1833 | 99.13 | 0.007 | 12 |
ITS1 | 638 | 64.42 | 679 | 63.04 | 692 | 46.24 | 0.599 | 254 |
5.8S rRNA | 157 | 57.96 | 157 | 57.96 | 157 | 100.00 | 0.000 | 0 |
ITS2 | 434 | 65.67 | 420 | 65.72 | 446 | 61.66 | 0.432 | 133 |
28S rRNA | 3633 | 57.68 | 3612 | 57.22 | 3638 | 96.65 | 0.025 | 90 |
IGS | 6216 | 61.18 | 5402 | 58.33 | 6239 | 40.47 | 0.878 | 2724 |
Species | Sub-Repeat | Width (bp) | Copy Number | Location | GC Content (%) | Entropy (0–2) |
---|---|---|---|---|---|---|
Ruditapes philippinarum | R-S1 | 36 | 3.8 | 592–727 | 55.65 | 1.99 |
R-S2 | 154 | 3 | 700–1161 | 54.55 | 1.98 | |
R-S3 | 4 | 29 | 2635–2752 | 75.00 | 1.49 | |
R-S4 | 62 | 2 | 3164–3284 | 63.64 | 1.90 | |
R-S5 | 72 | 1.9 | 3320–3454 | 65.75 | 1.89 | |
R-S6 | 141 | 2 | 4338–4619 | 65.96 | 1.91 | |
R-S7 | 72 | 1.9 | 4637–4771 | 65.75 | 1.89 | |
Mercenaria mercenaria | M-S1 | 48 | 3 | 3615–3761 | 66.67 | 1.89 |
M-S2 | 96 | 1.8 | 3599–3776 | 64.29 | 1.88 | |
M-S3 | 48 | 3 | 4054–4197 | 62.50 | 1.91 |
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Guo, Z.; Wang, Z.; Hou, X. Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria. Fishes 2021, 6, 42. https://doi.org/10.3390/fishes6030042
Guo Z, Wang Z, Hou X. Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria. Fishes. 2021; 6(3):42. https://doi.org/10.3390/fishes6030042
Chicago/Turabian StyleGuo, Zhansheng, Zhen Wang, and Xuguang Hou. 2021. "Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria" Fishes 6, no. 3: 42. https://doi.org/10.3390/fishes6030042