Journal Article

The complete mitochondrial genome of one breeding strain of Asian swamp eel (Monopterus albus, Zuiew 1793) using PacBio and Illumina sequencing technologies and phylogenetic analysis in synbranchiformes

Tian, H., Hu, Q., Lu, H. and Li, Z.

Record Number:
5520
Year:
2021
Journal:
Genes
Pages:
1-10
Volume:
12, 1567
Abstract:
Abstract: Asian swamp eel (Monopterus albus, Zuiew 1793) is a commercially important fish due to its nutritional value in Eastern and Southeastern Asia. One local strain of M. albus distributed in the Jianghan Plain of China has been subjected to a selection breeding program because of its preferred body color and superiority of growth and fecundity. Some members of the genus Monopterus have been reclassified into other genera recently. These classifications require further phylogenetic analyses. In this study, the complete mitochondrial genomes of the breeds of M. albus were decoded using both PacBio and Illumina sequencing technologies, then phylogenetic analyses were carried out, including sampling of M. albus at five different sites and 14 species of Synbranchiformes with complete mitochondrial genomes. The total length of the mitogenome is 16,621 bp, which is one nucleotide shorter than that of four mitogenomes of M. albus sampled from four provinces in China, as well as one with an unknown sampling site. The gene content, gene order, and overall base compositions are almost identical to the five reported ones. The results of maximum likelihood (ML) and Bayesian inference analyses of the complete mitochondrial genome and 13 protein-coding genes (PCGs) were consistent. The phylogenetic trees indicated that the selecting breed formed the deepest branch in the clade of all Asian swamp eels, confirmed the phylogenetic relationships of four genera of the family Synbranchidae, also providing systematic phylogenetic relationships for the order Synbranchiformes. The divergence time analyses showed that all Asian swamp eels diverged about 0.49 million years ago (MYA) and their common ancestor split from other species about 45.96 MYA in the middle of the Miocene epoch. Altogether, the complete mitogenome of this breed of M. albus would serve as an important dataset for germplasm identification and breeding programs for this species, in addition to providing great help in identifying the phylogenetic relationships of the order Synbranchiformes. Keywords: Monopterus albus; swamp eel; mitochondrial genome; PacBio; phylogenetic analysis; Synbranchiformes
Times Cited:
1
Related Records:
Mees, G.F. (1962)
The subterranean freshwater fauna of Yardie Creek Station, North West Cape, Western Australia
Richards, A. M. (1963)
The subterranean freshwater fauna of North West Cape, Western Australia
Cawthorn, P. (1963)
Discovery of subterranean freshwater fauna on the eastern side of North West Cape
Rosen, D. E. and Greenwood, P. H. (1976)
A fourth neotropical species of synbranchid eel and the phylogeny and systematics of synbranchiform fishes
Michaelis, F. (1985)
Threatened fish. A report on the threatened fish of inland waters of Austalia
Pollard, D. A., Ingram, B. A., Harris, J. H. and Reynolds, L. F. (1990)
Threatened fishes in Australia - an overview
Humphreys, W. F. and Adams, M. (1991)
The subterranean aquatic fauna of the North West Cape peninsula, Western Australia
Allen, G.R. (1992)
Inland Fishes of Western Australia
Adams, M. and Humphreys, W.F. (1993)
Patterns of genetic diversity within selected subterranean fauna of the Cape Range penninsula, Western Australia: Systematic and biogeographic implications
Knott, B. (1993)
Stygofauna of the Cape Range penninsula, Western Australia: Tethyan relicts
Humphreys, W. F. (1993)
The biogeography of Cape Range, Western Australia
Humphreys, W. F. (1993)
The significance of the subterranean fauna in biogeographical reconstruction: Examples from Cape Range Peninsula, Western Australia
Humphreys, W.F. (1994)
The subterranean fauna of the Cape Range coastal plane, Northwestern Australia
Humphreys, W. F. and Feinberg, M. N. (1995)
Food of the blind cave fishes of Northwestern Australia
Eberhard, S. and Hamilton-Smith, E. (1996)
Conservation of cave fauna in Australia
Hamilton-Smith, E., Kiernan, K. and Spate, A. (1996)
Karst management considerations for the Cape Range karst province, Western Australia
Yager, J. and Humphreys, W. F. (1996)
Lasionectes exleyi sp. nov. the first Remipede crustacean recorded from Australia and the Indian Ocean, with a key to the world species
Humphreys, W.F. (1997)
Protection of arid karstlands on the Cape Range Penninsula, Western Australia
Humphreys, W. F. (1999)
Physico-chemical profile and energy fixation in Bundera Sinkhole, an anchialine remiped habitat in north-western Australia
Humphreys, W. F. (1999)
The distribution of Australian cave fishes
Humphreys, W.F., Poole, A., Eberhard, S.M. and Warren, D. (1999)
Effects of research diving on the physico-chemical profile of Bundera Sinkhole, an anchialine remiped habitat at Cape Range, Western Australia
Humphreys, W.F. (2000)
The hypogean fauna of the Cape Range Peninsula and Barrow Island, northwestern Australia
Romero, A. and Vanselow, P.B.S. (2000)
Threatened fishes of the world: Ophisternon candidum (Mees, 1962) Synbranchidae
Romero, A. and Vanselow, P.B.S. (2000)
Threatened fishes of the world: Milyeringa veritas Whitley, 1945 (Eleotridae)
Jaume, D., Boxshall, G.A. and Humphreys, W.F. (2001)
New stygobiont copepods (Calanoida; Misophrioida) from Bundera sinkhole, an anchialine cenote on north-western Australia
Humphreys, W.R. (2001)
Groundwater calcrete aquifers in the Australian arid zone: the context to an unfolding plethora of stygal biodiversity
Wilson, R.S. and Humphreys, W.F. (2001)
Prionospio thalajani sp. nov. (Polychaeta: Spionidae) from an anchialine cave, Cape range, north-western Australia
Humphreys, W.F. (2001)
Milyeringa veritas (Eleotridae), a remarkably versatile cave fish from the arid tropics of northwestern Australia
Humphreys, WF (2001)
The subterranean fauna of Barrow island, northwestern Australia, and its environment
Unmack, P.J. (2001)
Biogeography of Australian freshwater fishes
Moore, B.P., Humphreys, W.F., Decu, V. and Juberthie, C. (2001)
Australie
Boulton, A.J., Humphreys, W,F. and Eberhard, S.M. (2003)
Imperilled subsurface waters in Ausralia: biodiversity, threatening processes and conservation
Eberhard, S.M., Halse, S.A. and Humphreys, W.F. (2005)
Stygofauna in the Pilbara region, north-west Western Australia: a review
Hancock, P.J., Boulton, A.J. and Humphreys, W.F. (2005)
Aquifers and hyporheic zones: Towards an ecological understanding of groundwater.
Humphreys, W.F., Shiao, J.-C., Iizuka, Y. and Tzeng, W.-N. (2006)
Can otolith microchemistry reveal whether the blind cave gudgeon, Milyeringa veritas (Eleotridae), is diadromous within a subterranean estuary?
Humphreys, W.F. (2006)
Aquifers: the ultimate groundwater-dependent ecosystems
Finston, T.L., Johnson, M.S., Humphreys, W.F., Eberhard, S.M. and Halse, S.A. (2007)
Cryptic speciation in two widespread subterranean amphipod genera reflects historical drainage patterns in an ancient landscape
Furter, E. (2007)
Underground life : environmental assessments just became more complicated
Humphreys, W.F. (2008)
Rising from down under: developments in subterranean biodiversity in Australia from a groundwater fauna perspective
Humphreys, W.F., Watts, C.H.S., Cooper, S.J.B. and Leijs, R. (2009)
Groundwater estuaries of salt lakes: buried pools of endemic biodiversity on the western plateau, Australia
Collins, L.B. and Stevens, A. (2010)
Assessment of coastal groundwater and linkages with Ningaloo Reef – final report February 2010
Department of the Environment, Water, Heritage and the Arts (2010)
Ningaloo Coast World Heritage nomination
Humphreys, W., Tetu, S., Elbourne, L., Gillings, M., Seymour, J., Mitchell, J. and Paulsen, I. (2012)
Geochemical and microbial diversity of Bundera Sinkhole, an anchialine system in the eastern Indian Ocean
Humphreys, W.F (2012)
Diversity patterns in Australia
Abrams, K. M., Guzik, M.T., Cooper, S.J.B., Humphreys, W.F., King, R.A., Cho J.L. and Austin, A.D. (2012)
What lies beneath: molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea)
Environmental Protection Authority (2012)
A review of subterranean fauna assessment in Western Australia. Discussion Paper. February 2012
Humphreys, G., Alexander, J., Harvey, M.S. and Humphreys, W.F. (2013)
The subterranean fauna of Barrow Island, northwestern Australia: 10 years on
Unmack, P.J. (2013)
Biogeography
Larson, H.K., Foster, R., Humphreys, W.F. and Stevens, M. (2013)
A new species of blind cave gudgeon Milyeringa (Pisces: Gobioidei, Eleotridaee) from Barrow Island, Western Australia, with a redescription of M. veritas Whitley
Morgan, D.L., Unmack, P.J., Beatty, S.J., Ebner, B.C., Allen, M.G., Keleher, J., Donaldson, J.A. and Murphy, J. (2014)
An overview of the 'freshwater fishes' of Western Australia
Halse, S., Scanlon, M., Cocking, J., Barron, H., Richardson, J. and Eberhard, S. (2014)
Pilbara stygofauna: deep groundwater of an arid landscape contains globally significant radiation of biodiversity
Bishop, R.E., Humphreys, W.F., Cukrov, N., Zic, V., Boxshall, G.A., Cukrov, M., Iliffe, T.M., Krsinic, F., Moore, W.S., Pohlman, J.W., and Sket, B. (2015)
‘Anchialine’ redefined as a subterranean estuary in a crevicular or cavernous geological setting
Humphreys, W. F. (2017)
Australasian subterranean biodiversity
Perina, G., Camacho, A.I., Huey, J., Horwitz, P., and Koenders, A. (2018)
Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach
Moore, G.I. (2018)
New morphological data and live photographs of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) from north‑western Australia
Moore, G.I., Humphreys, W.F. and Foster, R. (2018)
New populations of the rare subterranean Blind Cave Eel Ophisternon candidum (Synbranchidae) reveal recent historical connections throughout northwestern Australia
Page, T.J., Hughes, J.M., Real, K.M., Stevens, M.I., King, R.A. and Humphreys, W.F. (2018)
Allegory of a cave crustacean: systematic and biogeographic reality of Halosbaena (Peracarida: Thermosbaenacea) sought with molecular data at multiple scales
Halse, S. (2018)
Subterranean fauna of the arid zone
Page, T.J.,Stevens, M.I., Adams, M., Foster, R. Velasco-Castrillón, A. and Humphreys, W.F. (2018)
Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)
Perina, G., Camacho, A.I., Huey, J., Horwitz, P. and Koenders, A. (2019)
New Bathynellidae (Crustacea) taxa and their relationships in the Fortescue catchment aquifers of the Pilbara region, Western Australia, Systematics and Biodiversity
Perina, G., Camacho, A., Huey, J., Horwitz, P. and Koenders, A. (2019)
The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
Matthews, E.F., Abrams, K.M., Cooper, S.J.B., Huey, J.A., Hillyer, M.J., Humphreys, W.F., Austin, A.D. and Guzik, M.T. (2019)
Scratching the surface of subterranean biodiversity: molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia
Perina, G. (2019)
Ancient origins of a diverse stygofaunal group: The Australian Bathynellidae (Crustacea)
Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z. and Garnett, S.T. (2020)
Big trouble for little fish: identifying Australian freshwater fishes in imminent risk of extinction
White, N.E., Guzik, M.T., Austin, A.D., Moore, G.I. Humphreys, W.F., Alexander, J. and Bunce, M. (2020)
Detection of rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments
Shelley, J.J., Swearer, S.E., Dempster, T., Adams, M., Le Feuvre, M.C., Hammer, M.P. and Unmack, P.J. (2020)
Plio-Pleistocene sea-level changes drive speciation of freshwater fishes in north-western Australia
Eberhard, S.M. and Howarth, F.G. (2021)
Undara lava cave fauna in tropical Queensland with an annotated list of Australian subterranean biodiversity hotspots
Tian, H., Hu, Q., Lu, H. and Li, Z. (2021)
The complete mitochondrial genome of one breeding strain of Asian swamp eel (Monopterus albus, Zuiew 1793) using PacBio and Illumina sequencing technologies and phylogenetic analysis in synbranchiformes
Saccò, M., Guzik, M.T., van der Heyde, M., Nevill, P., Cooper, S.J.B., Austin, A.D., Coates, P.J. and Allentoft, M.E. (2022)
eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects
Saccò, M., Blyth, A.J., Douglas, G., Humphreys, W.F., Hose, G.C., Davis, J., Guzik, M.T., Martínez, A., Eberhard, S.M. and Halse, S.A. (2022)
Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm
Webb, J.A., White, S.Q. and Smith, G.K. (2023)
Australian caves and karst systems
White, S.Q., Brooks, D. and Webb, J.A. (2023)
Cape Range
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)
Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater
van der Heyde, M., Alexander, J., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)
Rapid detection of subterranean fauna from passive sampling of groundwater eDNA