The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae)
- Global styles
- MLA
- Vancouver
- Elsevier - Harvard
- APA
- Help

View/ Open
Date
2024-04-02Page views
626ASFA keyword
AGROVOC keyword
Taxonomic term
Metadata
Perlihat publikasi penuh
Share
Abstract
This study presents the complete mitochondrial genome sequence of Gammarus nipponensis, a freshwater crustacean found in the western regions of Honshu, Shikoku and Kyushu in Japan. The entire genome is 16,429 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, as well as the putative control regions. The mitochondrial genome of G. nipponensis is characterized by a high concentration of A and T nucleotides (67.1%). Notably, the mitogenome contains long TATTTTA repeats in the control region 2 at 686 bp long. This newly available genome information will be useful for studying the evolutionary relationships within the genus Gammarus and for understanding diversification among G. nipponensis populations.
Keywords
Complete mitogenome amphipods Gammaroidea phylogenySubjects
Mitochondrial DNASuggested Citation
Huervana, J. J., Miyamoto, N., Kano, Y., Onikura, N., & Kurita, Y. (2024). The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae). Mitochondrial DNA Part B , 9(4), 447-451. https://doi.org/10.1080/23802359.2024.2335990
Type
ArticleISSN
2380-2359Koleksi
- Journal Articles [1266]
Related items
Showing items related by title, author, creator and subject.
-
Preliminary assessment of genetic variation in the Japanese endemic freshwater crab, Geothelphusa dehaani, based on mitochondrial DNA sequences
Huervana, Joana Joy
; Kano, Yuichi
; Ando, Daiki; Onikura, Norio
; Kurita, Yoshihisa (Pensoft Publishers, 2023-06-27)
Geothelphusa dehaani, a freshwater crab species endemic to Japan, has the largest distribution range amongst the 19 known species in the country. Due to its low dispersal capability and restricted habitat to freshwater, it serves as an excellent model for understanding gene flow between geographically isolated populations. In this study, we analysed the genetic relationships of 26 G. dehaani populations collected from different locations in the Japanese archipelago using two mitochondrial DNA regions - cytochrome oxidase subunit I (COI) and cytochrome b (cytB). Our results from the analysis of molecular variance (AMOVA) revealed high genetic variation amongst populations and the phylogenetic analysis identified four geographical groups: Clade I - Honshu and Shikoku, Clade II - north-eastern Kyushu, Clade III - southern Kyushu and Clade IV - north-western Kyushu. Notably, Clade IV exhibited the highest genetic distance amongst the observed groupings. These findings highlight the need for further examination of G. dehaani in Kyushu, including morphological and behavioural traits, to better understand the observed diversity within the species in the region. -
Characterization of wild eucheumatoids from Visayas, Philippines as inferred from the mitochondrial cox2-3 spacer sequence
Sibonga, Rema
; Brakel, Janina
; Gachon, Claire
; Faisan, Joseph P., Jr.
; Brodie, Juliet
; Ward, Georgia
; Ferriols, Victor Marco Emmanuel
; Luhan, Maria Rovilla
; Hurtado, Anicia Q. (University of the Philippines Visayas, 2022)
Eucheumatoids are the major seaweed species cultivated in most coastal areas in the Philippines, being a major source of income for many families. Seaweed farmers face issues such as lack of good quality cultivars and the presence of diseases and epiphytes in the cultivated stocks. This study characterizes the wild eucheumatoids, which are potential sources of cultivars that might be resistant to diseases and epiphytes. Wild eucheumatoids were collected from Iloilo (N=18), Guimaras (N=10), and Bohol (N=20), Philippines. Gross morphology was described, and a 10-mm apical tip was excised for DNA extraction. PCR amplification and sequencing using cox2-3 spacer genetic markers were done. Based on sequence data, 5 species can be identified from the Visayas region: the commercially cultivated Kappaphycus alvarezii (Iloilo, Bohol), K. striatus (Iloilo, Guimaras), and Eucheuma denticulatum (Iloilo, Bohol) and the currently uncultivated K. cottonii (Iloilo) and Kappaphycus sp. (Iloilo, Bohol). Haplotype network analysis identifies individuals of K alvarezii and E. denticulatum as haplotype E3 and E13, respectively, which are haplotypes previously reported from seaweed farms and globally distributed for cultivation purposes. The K. striatus from Iloilo and Guimaras are identified as haplotype E89, and the K. cottonii from Iloilo is haplotype E108 which has been described previously from seaweed farms and wild populations, respectively. Interestingly, Kappaphycus sp. from Iloilo and Bohol are identified as haplotype GUI1 initially described in 2014 and yet to be identified up to the species level. Our study shows that purely morphological identification is not sufficient to reliably identify species, thus highlighting the need to employ molecular techniques supporting strain selection. In summary, it reveals a rich diversity of wild eucheumatoids in the Visayas region of the Philippines. In-vitro studies need to reveal the performance of individuals from these wild populations but highlight a great potential for the development of new cultivars. -
Genetic diversity in farmed Asian Nile and red hybrid tilapia stocks evaluated from microsatellite and mitochondrial DNA analysis
Romana-Eguia, Maria Rowena R.
; Ikeda, Minoru; Basiao, Zubaida U.; Taniguchi, Nobuhiko (Elsevier, 2004)
We analyzed microsatellite and mitochondrial DNA restriction fragment length polymorphism (mtDNA-RFLP) in two domesticated (NIFI and Israel) and four genetically improved (GIFT, GMT, FAC-selected and SEAFDEC-selected) Nile tilapia (Oreochromis niloticus) as well as five red hybrid tilapia (Oreochromis mossambicus × O. niloticus) stocks (BFS, FACred, NIFIred, HL, and PF) farmed in Asia. Microsatellite variation at five loci (UNH216, UNH172, UNH123, UNH147, UNH222) was more informative in characterizing stock differences than the mtDNA-RFLP markers that were based only on 14 restriction morphs. Contemporary microsatellite data showed that GIFT Nile tilapia had the highest mean expected heterozygosity (H>e=0.813), while GMT had the lowest (He=0.666). The unselected NIFI stock and SEAFDEC-selected were genetically similar, while GMT differed significantly from the other Nile tilapia stocks. Among the red tilapias, NIFIred had the highest He (0.715), while BFS had the lowest variability (He=0.567). The Taiwanese red tilapia HL and Thai NIFIred were genetically similar. Except for NIFI, most of the Nile and red tilapia stocks exhibited remarkably significant homozygote excess relative to Hardy–Weinberg Equilibrium (HWE), suggesting some degree of inbreeding. Asian Nile tilapias were more genetically diverse (pooled He=0.791; mtDNA nucleotide divergence value dA=0.009) than the red tilapias (pooled He=0.697; mean dA=0.004). This slight divergence between the Nile and red tilapias was also seen in the analysis of molecular variance (AMOVA; FCT=0.0018) and in genetic distance and nucleotide divergence dendrograms. However, the AMOVA revealed that the greater percentage of variation (99.33%) in the total genetic diversity of the surveyed stocks is principally due to differences at the individual level and not between nor within groups. The significance of these results is that they reflect and lead to new inferences regarding the selective breeding and culture methods used in managing these farmed stocks.






