Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei
Thuy Yen Duong
College of Aquaculture and Fisheries, Can Tho University, 3/2 street, Can Tho City, Vietnam.
Linh Thi Khanh Pham
Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam
Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
Xuyen Thi Kim Le
Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam
Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
Ngoc Tran Thi Nguyen
College of Aquaculture and Fisheries, Can Tho University, 3/2 street, Can Tho City, Vietnam.
Siti Azizah Mohd Nor
Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
Thanh Hoa Le
Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam
Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
Communicated by Ka Hou Chu
Pangasiidae (catfish order: Siluriformes) comprises 30 valid catfish species in four genera: Pangasius, Pangasianodon, Helicophagus, and Pseudolais. Their systematics are frequently revised due to the addition of newly described species. Although Pangasiidae is known to be a monophyletic family, the generic and phylogenetic relationships among the taxa are poorly resolved. This study characterized three newly obtained complete mitogenomes of Mekong River catfishes from Vietnam (Pangasius mekongensis, Pangasius krempfi, and Pangasianodon hypophthalmus), as well as the inter- and intrafamilial relationships of the Pangasiidae and catfish families in Siluroidei. The genomic features of their mitogenomes were similar to those of previously reported pangasiids, including all regulatory elements, extended terminal associated sequences (ETAS), and conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, and CSBs, A to F) in the control region. A comprehensive phylogeny constructed from datasets of multiple 13 PCG sequences from 117 complete mitogenomes of 32 recognized siluriform families established Pangasiidae as monophyletic and a sister group of Austroglanididae. The [Pangasiidae + Austroglanididae] + (Ictaluridae + Cranoglanididae) + Ariidae] clade is a sister to the “Big Africa” major clade of Siluriformes. Furthermore, both phylogenies constructed from the single barcodes (83 partial cox1 and 80 partial cytB, respectively) clearly indicate genus relationships within Pangasiidae. Pangasianodon was monophyletic and a sister to the (Pangasius + Helicophagus + Pseudolais) group. Within the genus Pangasius, P. mekongensis was placed as a sister taxon to P. pangasius. Pangasius sanitwongsei was found to be related to and grouped with Pangasianodon, but in single-gene phylogenies, it was assigned to the Pangasius + Helicophagus + Pseudolais group. The datasets in this study are useful for studying pangasiid systematics, taxonomy and evolution.
Supplementary materials
Alignment of ten control region sequences from eight species,
Pangasius mekongensis (Pmek),
Pangasius krempfi (Pkre),
Pangasius pangasius (Ppan),
Pangasius larnaudii (Plar),
Pangasius bocourti (Pboc),
Pangasius sanitwongsei (Psan),
Pangasianodon hypophthalmus (Phyp, three sequences), and
Pangasianodon gigas (Pgig). Types of conserved sequence blocks (CSBs) within a species (CSB-C), within a genus (CSB-B), and within both genera (
Pangasius and
Pangasianodon) (CSB-A) are presented. Aligned nucleotide sequences and typical CSBs are shown as boxes. For species, see table S2; for descriptions of the blocks, see text.
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Primers for amplification and sequencing of fragments of the mitochondrial genome of
Pangasiusmekongensis,
Pangasianodon hypophthalmus, and
Pangasius krempfi of the Mekong River, Vietnam.
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List and information of 117 siluriform sequences (109 species in 32 families) and two outgroup species with complete mitogenomes providing 13 protein-coding sequences used in this study for phylogenetic and sequence analysis of catfishes of the Pangasiidae and families in the order Siluriformes.
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Accession numbers and country report for the reference
cox1 and
cytB markers from the GenBank database and those from this study used for the pangasiid comparative phylogenetic studies.
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Nucleotide composition and skewness value for the complete mitochondrial genome (mtDNA) and the protein-coding genes (PCGs) of seven species members of the family Pangasiidae.
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Pairwise nucleotide differences (%) among five catfish species of the family Pangasiidae present in the Mekong Basin for individual mitochondrial protein- coding genes and mitochondrial ribosomal genes (12S and 16S).
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Pairwise genetic distances (%) estimated between
Pangasius mekongensis,
Pangasianodon hypophthalmus,
Pangasius krempfi, and the published or GenBank-deposited representative Pangasiidae species based on mitogenome coding nucleotide sequences.
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