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4 results for “Pangasiidae”
Fig. 3 in Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei.
Fig. 3. Detailed PhyML-phylogeny based on the analysis of the partial cox1 sequences (551 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 83 sequences, including 81 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Gymnotiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Karinthanyakit and Jondeung 2012; Tran and Duong 2019; Schedel et al. 2022). The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site.
Fig. 2 in Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei.
Fig. 2. PhyML-phylogeny of the order Siluriformes, including 32 catfish families (117 sequences) of three suborders, Siluroidei, Loricarioidei, and Diplomystoidei based on the complete concatenated nucleotide sequences of all 13 mitochondrial protein coding genes (about 11,408 bp in length) (Table S2). Two sequences of Gonorynchiformes were used as an outgroup. The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The nodal bootstrap support values (shown at each node) were interpreted from the concurrently constructed tree using the above MAFFT-BMGE alignment by MEGA X (Kumar et al. 2018). The basal nodes of the three suborders (Diplomystoidei, Loricarioidei, and Siluroidei) as well as the two major "Big Asia" and "Big Africa" groups (background highlighted) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are indicated by stars and with the associated families' background highlighted. The taxa were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Saitoh et al. 2003; Nakatani et al. 2011; Kappas et al. 2016; Zhang et al. 2021; Schedel et al. 2022). The country of origin or geographical regions where the sample was reported are given in full name, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site.
Fig. 1. A in Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei.
Fig. 1. A schematic circular map of the mitochondrial genome of three Mekong River pangasiid catfishes catfishes in Vietnam, Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi, and the OL origin site of the light (L) strand's replication. A, The circular map and gene abbreviations were generated by the MitoAnnotator software in the MitoFish database (http://mitofish.aori.u-tokyo.ac.jp/annotation/ input.html). Protein-coding genes (PCGs) are denoted by two capital letters or full names, and transfer RNA genes (tRNAs) are marked with threeletter amino-acid abbreviations. The heavy (H) strand is indicated by the outer line of the circle and the light (L) strand by the inner line. The D-loop (control region) is located between tRNAPro and tRNAPhe. The pangasiid photos were taken by the authors from the naturally caught fish on site. B, A schematic presentation of the stem-loop secondary structure of the OL origin site in mitogenomes of three pangasiid species based on the RNAfold predicted structure with the lowest free energy (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi). On the L-strand, between the two flanking tRNAs (trnN (c) and trnC (c)), there is a conserved stem (hairpin) formed by 9-nucleotide (nt) base-pairing and ending with a loop of 9 nt (in Pmek and Phyp) and 10 nt (in Pkre).
Fig. 4 in Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei.
Fig. 4. Detailed PhyML-phylogeny based on the analysis of the partial cytB sequences (634 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 80 sequences, including 78 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Clupeiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies. The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site.
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