Complete mitochondrial genome and phylogenetic position of  Pangasius sanitwongsei  (Siluriformes: Pangasiidae)

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Abstract

In this study, the complete mitochondrial genome of Pangasius sanitwongsei was firstly reported and analyzed. It had a double-stand DNA molecule with 16536 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region. The structural organization and gene order was similar to other bony fishes. The complete mitochondrial genome of P. sanitwongsei provided in this work would be helpful for further research on phylogenetics and conservation genetics of the Siluriformes and other orders.

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Prospects for inferring very large phylogenies by using the neighbor-joining method.

K Tamura, M Nei, S. Kumar (2004)

Current efforts to reconstruct the tree of life and histories of multigene families demand the inference of phylogenies consisting of thousands of gene sequences. However, for such large data sets even a moderate exploration of the tree space needed to identify the optimal tree is virtually impossible. For these cases the neighbor-joining (NJ) method is frequently used because of its demonstrated accuracy for smaller data sets and its computational speed. As data sets grow, however, the fraction of the tree space examined by the NJ algorithm becomes minuscule. Here, we report the results of our computer simulation for examining the accuracy of NJ trees for inferring very large phylogenies. First we present a likelihood method for the simultaneous estimation of all pairwise distances by using biologically realistic models of nucleotide substitution. Use of this method corrects up to 60% of NJ tree errors. Our simulation results show that the accuracy of NJ trees decline only by approximately 5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio. Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies.

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ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.

Dean Laslett, Björn Canbäck (2008)

Mitochondrial genomes encode their own transfer RNAs (tRNAs). These are often degenerate in sequence and structure compared to tRNAs in their bacterial ancestors. This is one of the reasons why current tRNA gene predictor programs perform poorly identifying mitochondrial tRNA genes. As a consequence there is a need for a new program with the specific aim of predicting these tRNAs. In this study, we present the software ARWEN that identifies tRNA genes in metazoan mitochondrial nucleotide sequences. ARWEN detects close to 100% of previously annotated genes. An online version, software for download and test results are available at www.acgt.se/online.html

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Asian river fishes in the Anthropocene: threats and conservation challenges in an era of rapid environmental change.

D Dudgeon (2011)

This review compares and contrasts the environmental changes that have influenced, or will influence, fishes and fisheries in the Yangtze and Mekong Rivers. These two rivers have been chosen because they differ markedly in the type and intensity of prevailing threats. The Mekong is relatively pristine, whereas the Three Gorges Dam on the Yangtze is the world's largest dam representing the apotheosis of environmental alteration of Asian rivers thus far. Moreover, it is situated at the foot of a planned cascade of at least 12 new dams on the upper Yangtze. Anthropogenic effects of dams and pollution of Yangtze fishes will be exacerbated by plans to divert water northwards along three transfer routes, in part to supplement the flow of the Yellow River. Adaptation to climate change will undoubtedly stimulate more dam construction and flow regulation, potentially causing perfect storm conditions for fishes in the Yangtze. China has already built dams along the upper course of the Mekong, and there are plans for as many as 11 mainstream dams in People's Democratic Republic (Laos) and Cambodia in the lower Mekong Basin. If built, they could have profound consequences for biodiversity, fisheries and human livelihoods, and such concerns have stalled dam construction. Potential effects of dams proposed for other rivers (such as Nujiang-Salween) are also cause for concern. Conservation or restoration measures to sustain some semblance of the rich fish biodiversity of Asian rivers can be identified, but their implementation may prove problematic in a context of increasing Anthropocene alteration of these ecosystems. © 2011 The Author. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

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Journal

Journal ID (nlm-ta): Mitochondrial DNA B Resour

Journal ID (iso-abbrev): Mitochondrial DNA B Resour

Title: Mitochondrial DNA. Part B, Resources

Publisher: Taylor & Francis

ISSN (Electronic): 2380-2359

Publication date (Electronic, pub): 31 January 2020

Publication date (Electronic, collection): 2020

Volume: 5

Issue: 1

Pages: 945-946

Affiliations

Aquatic Species Introduction and Breeding Center of Guangxi , Nanning, China

Author notes

CONTACT Sheng Zhang 20749078@ 123456qq.com Aquatic Species Introduction and Breeding Center of Guangxi , 30 BaiSha Road, Nanning530031, China.

Article

Publisher ID: 1719915

DOI: 10.1080/23802359.2020.1719915

PMC ID: 7748851

SO-VID: 497d5ca9-eb22-4e6e-8f77-4a1da4ea7391

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Complete mitochondrial genome and phylogenetic position of Pangasius sanitwongsei (Siluriformes: Pangasiidae)

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Genome Integrity

Most cited references 6

Prospects for inferring very large phylogenies by using the neighbor-joining method.

ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.

Asian river fishes in the Anthropocene: threats and conservation challenges in an era of rapid environmental change.

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