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Islam R, Rahman A. An alignment-free method for detection of missing regions for phylogenetic analysis. Heliyon 2024; 10:e32227. [PMID: 38933968 PMCID: PMC11200290 DOI: 10.1016/j.heliyon.2024.e32227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Phylogenetic tree estimation using conventional approaches usually requires pairwise or multiple sequence alignment. However, sequence alignment has difficulties related to scalability and accuracy in case of long sequences such as whole genomes, low sequence identity, and in presence of genomic rearrangements. To address these issues, alignment-free approaches have been proposed. While these methods have demonstrated promising results, many of these lead to errors when regions are missing from the sequences of one or more species that are trivially detected in alignment-based methods. Here, we present an alignment-free method for detecting missing regions in sequences of species for which phylogeny is to be estimated. It is based on counts of k-mers and can be used to filter out k-mers belonging to regions in one species that are missing in one or more of the other species. We perform experiments with real and simulated datasets containing missing regions and find that it can successfully detect a large fraction of such k-mers and can lead to improvements in the estimated phylogenies. Our method can be used in k-mer based alignment-free phylogeny estimation methods to filter out k-mers corresponding to missing regions.
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Affiliation(s)
- Rubyeat Islam
- Department of Computer Science and Engineering, Military Institute of Science and Technology, Dhaka, Bangladesh
| | - Atif Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
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Duong TY, Pham LTK, Le XTK, Nguyen NTT, Nor AM, Le TH. Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei. Zool Stud 2023; 62:e48. [PMID: 37965298 PMCID: PMC10641430 DOI: 10.6620/zs.2023.62-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/24/2023] [Indexed: 11/16/2023]
Abstract
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.
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Affiliation(s)
- Thuy Yen Duong
- College of Aquaculture and Fisheries, Can Tho University, 3/2 street, Can Tho City, Vietnam. E-mail: (Duong)
| | - 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. E-mail: (Le); (Pham); (Kim Le)
- 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. E-mail: (Le); (Pham); (Kim Le)
- 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. E-mail: (Duong)
| | - Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia. E-mail: (Nor)
| | - 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. E-mail: (Le); (Pham); (Kim Le)
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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Zhang Z, Li J, Zhang X, Lin B, Chen J. Comparative mitogenomes provide new insights into phylogeny and taxonomy of the subfamily Xenocyprinae (Cypriniformes: Cyprinidae). Front Genet 2022; 13:966633. [DOI: 10.3389/fgene.2022.966633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Xenocyprinae is a cyprinid subfamily that not only has a discrete geographic distribution but also has a long history dating to the Early Miocene. However, it is controversial whether systematic classification and some species validity of Xenocyprinae exist, as well as its phylogenetic relationships and evolutionary history. In the present study, we first reviewed the description and taxonomic history of Xenocyprinae, and then the complete mitochondrial genome of Distoechodon compressus, an endemic and locally distributed species belonging to Xenocyprinae, was sequenced and annotated. Finally, all the mitogenomes of Xenocyprinae were compared to reconstruct the phylogenetic relationship and estimate the divergence time. The results showed that the mitogenomes are similar in organization and structure with 16618–16630 bp length from 12 mitogenomes of eight species. Phylogenetic analysis confirmed the monology of Xenocyprinae and illustrated three clades within the Xenocyprinae to consist of ambiguous generic classification. Plagiognathops is a valid genus located at the base of the phylogenetic tree. The genus Xenocypris was originally monophyletic, but X. fangi was excluded. Divergence time estimation revealed that the earliest divergence within Xenocyprinae occurred approximately 12.1 Mya when Plagiognathops separated from the primitive Xenocypris. The main two clades (Xenocypris and (Distoechodon + Pseudobrama + X. fangi)) diverged 10.0 Mya. The major divergence of Xenocyprinae species possibly occurred in the Middle to Late Miocene and Late Pliocene, suggesting that speciation and diversifications could be attributed to the Asian monsoon climate. This study clarifies some controversial issues of systematics and provides essential information on the taxonomy and phylogeny of the subfamily Xenocyprinae.
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Protocol for correlation analysis of the murine gut microbiome and meta-metabolome using 16S rDNA sequencing and UPLC-MS. STAR Protoc 2022; 3:101494. [PMID: 35776638 PMCID: PMC9250040 DOI: 10.1016/j.xpro.2022.101494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/13/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The gut microbiota and metabolites play pivotal roles in the pathobiology of various diseases. Here, we describe a protocol to profile the gut microbiome and meta-metabolome of a mouse disease model for acute graft-versus-host disease. We describe steps for fecal sample collection and processing for 16S sequencing and UPLC-MS. Finally, we detail the steps for data analysis and exhibit multi-omic associations to correlate with pathology. For complete details on the use and execution of this protocol, please refer to Li et al. (2020). Fecal 16S rDNA gene sequencing and LC-MS decodes gut microenvironment during disease Screening and correlation analysis between microbiome and metabolome Joint analysis of multi-omics data and correlation with pathology
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Zhang Y, Wang M, Cheng R, Luo Y, Li Y, Liu Z, Chen Q, Shen Y. Mitochondrial characteristics of Pseudohynobius flavomaculatus a protected salamander in China, and biogeographical implications for the family Hynobiidae (Amphibia, Caudata). ZOOSYST EVOL 2022. [DOI: 10.3897/zse.98.66578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pseudohynobius flavomaculatus a provincially-protected salamander species, inhabits mountainous areas of Chongqing and surrounding provinces in China. In the present study, the complete mitochondrial genome of P. flavomaculatus was sequenced and analyzed. The mitogenome is 16,401 bp in length and consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. We performed a novel phylogenetic analysis, which demonstrated a sister relationship between P. flavomaculatus and P. jinfo. The 95% confidence interval around our new divergence date estimate suggest that Hynobiidae originated at 101.62–119.84 (mean=110.87) Ma. Species within Hynobiidae diverged successively in the Cenozoic era, and hynobiid speciation coincides primarily with geologic events. Our biogeographical inference demonstrates that nearly all early hynobiids divergences correspond to geological estimates of orogeny, which may have contributed to the notably high dN/dS ratio in this clade. We conclude that orogeny is likely a primary, dynamic factor, which may have repeatedly initiated the process of speciation in the family Hynobiidae.
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Zhang Z, Li S, Zhang J, Song W, Yang J, Mu J. The complete mitochondrial genome of an endangered minnow Aphyocypris lini (Cypriniformes: Xenocyprididae): genome characterization and phylogenetic consideration. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00811-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Fischer C, Koblmüller S, Börger C, Michelitsch G, Trajanoski S, Schlötterer C, Guelly C, Thallinger GG, Sturmbauer C. Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. Sci Rep 2021; 11:4309. [PMID: 33619328 PMCID: PMC7900123 DOI: 10.1038/s41598-021-81030-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/28/2020] [Indexed: 01/01/2023] Open
Abstract
With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3-9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.
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Affiliation(s)
- C Fischer
- Institute of Biology, University of Graz, Graz, Austria
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - S Koblmüller
- Institute of Biology, University of Graz, Graz, Austria
| | - C Börger
- Institute of Biology, University of Graz, Graz, Austria
| | - G Michelitsch
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - S Trajanoski
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - C Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - C Guelly
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - G G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - C Sturmbauer
- Institute of Biology, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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Lv W, Jiang H, Bo J, Wang C, Yang L, He S. Comparative mitochondrial genome analysis of Neodontobutis hainanensis and Perccottus glenii reveals conserved genome organization and phylogeny. Genomics 2020; 112:3862-3870. [DOI: 10.1016/j.ygeno.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 10/23/2022]
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Delibaş E, Arslan A, Şeker A, Diri B. A novel alignment-free DNA sequence similarity analysis approach based on top-k n-gram match-up. J Mol Graph Model 2020; 100:107693. [PMID: 32805559 DOI: 10.1016/j.jmgm.2020.107693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/15/2020] [Accepted: 07/06/2020] [Indexed: 11/17/2022]
Abstract
DNA sequence similarity analysis is an essential task in computational biology and bioinformatics. In nearly all research that explores evolutionary relationships, gene function analysis, protein structure prediction and sequence retrieving, it is necessary to perform similarity calculations. As an alternative to alignment-based sequence comparison methods, which result in high computational cost, alignment-free methods have emerged that calculate similarity by digitizing the sequence in a different space. In this paper, we proposed an alignment-free DNA sequence similarity analysis method based on top-k n-gram matches, with the prediction that common repeating DNA subsections indicate high similarity between DNA sequences. In our method, we determined DNA sequence similarities by measuring similarity among feature vectors created according to top-k n-gram match-up scores without the use of similarity functions. We applied the similarity calculation for three different DNA data sets of different lengths. The phylogenetic relationships revealed by our method show that our trees coincide almost completely with the results of the MEGA software, which is based on sequence alignment. Our findings show that a certain number of frequently recurring common sequence patterns have the power to characterize DNA sequences.
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Affiliation(s)
- Emre Delibaş
- Department of Computer Engineering, Faculty of Engineering, Sivas Cumhuriyet University, 58140, Sivas, Turkey.
| | - Ahmet Arslan
- Department of Computer Engineering, Faculty of Engineering, Selçuk University, 42250, Konya, Turkey.
| | - Abdulkadir Şeker
- Department of Computer Engineering, Faculty of Engineering, Sivas Cumhuriyet University, 58140, Sivas, Turkey.
| | - Banu Diri
- Department of Computer Engineering, Faculty of Electrical and Electronics, Yıldız Technical University, 34349, Ístanbul, Turkey.
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Röhling S, Linne A, Schellhorn J, Hosseini M, Dencker T, Morgenstern B. The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances. PLoS One 2020; 15:e0228070. [PMID: 32040534 PMCID: PMC7010260 DOI: 10.1371/journal.pone.0228070] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
We study the number Nk of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences-i.e. the number of substitutions per site that occurred since they evolved from their last common ancestor-can be estimated from the slope of a function F that depends on Nk and that is affine-linear within a certain range of k. Integers kmin and kmax can be calculated depending on the length of the input sequences, such that the slope of F in the relevant range can be estimated from the values F(kmin) and F(kmax). This approach can be generalized to so-called Spaced-word Matches (SpaM), where mismatches are allowed at positions specified by a user-defined binary pattern. Based on these theoretical results, we implemented a prototype software program for alignment-free sequence comparison called Slope-SpaM. Test runs on real and simulated sequence data show that Slope-SpaM can accurately estimate phylogenetic distances for distances up to around 0.5 substitutions per position. The statistical stability of our results is improved if spaced words are used instead of contiguous words. Unlike previous alignment-free methods that are based on the number of (spaced) word matches, Slope-SpaM produces accurate results, even if sequences share only local homologies.
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Affiliation(s)
- Sophie Röhling
- University of Göttingen, Department of Bioinformatics, Göttingen, Germany
| | - Alexander Linne
- University of Göttingen, Department of Bioinformatics, Göttingen, Germany
| | - Jendrik Schellhorn
- University of Göttingen, Department of Bioinformatics, Göttingen, Germany
| | | | - Thomas Dencker
- University of Göttingen, Department of Bioinformatics, Göttingen, Germany
| | - Burkhard Morgenstern
- University of Göttingen, Department of Bioinformatics, Göttingen, Germany
- Göttingen Center of Molecular Biosciences (GZMB), Göttingen, Germany
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12
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Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi JJ, Waterman MS, Comin M, Kim SH, Vinga S, Almeida JS, Chan CX, James BT, Sun F, Morgenstern B, Karlowski WM. Benchmarking of alignment-free sequence comparison methods. Genome Biol 2019; 20:144. [PMID: 31345254 PMCID: PMC6659240 DOI: 10.1186/s13059-019-1755-7] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. RESULTS Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. CONCLUSION The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.
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Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Hani Z Girgis
- Tandy School of Computer Science, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK, 74104, USA
| | | | - Chris-Andre Leimeister
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Kujin Tang
- Department of Biological Sciences, Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Thomas Dencker
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Anna Katharina Lau
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Sophie Röhling
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Jae Jin Choi
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michael S Waterman
- Department of Biological Sciences, Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, 200433, China
| | - Matteo Comin
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Sung-Hou Kim
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Susana Vinga
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NIH/NCI), Bethesda, USA
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin T James
- Tandy School of Computer Science, The University of Tulsa, 800 South Tucker Drive, Tulsa, OK, 74104, USA
| | - Fengzhu Sun
- Department of Biological Sciences, Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA
- Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, 200433, China
| | - Burkhard Morgenstern
- Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Wojciech M Karlowski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
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Rapid divergence, molecular evolution, and morphological diversification of coastal host-parasite systems from southern Brazil. Parasitology 2019; 146:1313-1332. [PMID: 31142390 DOI: 10.1017/s0031182019000556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study assessed the role of historical processes on the geographic isolation, molecular evolution, and morphological diversification of host-parasite populations from the southern Brazilian coast. Adult specimens of Scleromystax barbatus and Scleromystax macropterus were collected from the sub-basin of the Nhundiaquara River and the sub-basin of the Paranaguá Bay, state of Paraná, Brazil. Four species of Gyrodactylus were recovered from the body surface of both host species. Morphometric analysis of Gyrodactylus spp. and Scleromystax spp. indicated that subpopulations of parasites and hosts could be distinguished from different sub-basins and locations, but the degree of morphological differentiation seems to be little related to geographic distance between subpopulations. Phylogenetic relationships based on DNA sequences of Gyrodactylus spp. and Scleromystax spp. allowed distinguishing lineages of parasites and hosts from different sub-basins. However, the level of genetic structuring of parasites was higher in comparison to host species. Evidence of positive selection in mtDNA sequences is likely associated with local adaptation of lineages of parasites and hosts. A historical demographic analysis revealed that populations of Gyrodactylus and Scleromystax have expanded in the last 250 000 years. The genetic variation of parasites and hosts is consistent with population-specific selection, population expansions, and recent evolutionary co-divergence.
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Chen S, Tang Q. The complete mitochondrial genome of big-eye mandarin fish Siniperca kneri (perciformes: Sinipercidae) from Hanjiang river. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Suwei Chen
- School of Modern Agriculture and Biotechnology, Ankang University, Ankang, China
| | - Qiongying Tang
- College of Life Science, Huzhou University, Huzhou, China
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15
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Bbole I, Zhao JL, Tang SJ, Katongo C. Mitochondrial genome annotation and phylogenetic placement of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa. PLoS One 2018; 13:e0203095. [PMID: 30481181 PMCID: PMC6258479 DOI: 10.1371/journal.pone.0203095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022] Open
Abstract
Genetic characterization of southern African cichlids has not received much attention. Here, we describe the mitogenome sequences and phylogenetic positioning of Oreochromis andersonii and O. macrochir among the African cichlids. The complete mitochondrial DNA sequences were determined for O. andersonii and O. macrochir, two important aquaculture and fisheries species endemic to southern Africa. The complete mitogenome sequence lengths were 16642 bp and 16644 bp for O. andersonii and O. macrochir respectively. The general structural organization follows that of other teleost species with 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a non-coding control region. Phylogenetic placement of the two species among other African cichlids was performed using Maximum Likelihood (ML) and Bayesian Markov-Chain-Monte-Carlo (MCMC). The consensus trees confirmed the relative positions of the two cichlid species with O. andersonii being very closely related to O. mossambicus and O. macrochir showing a close relation to both species. Among the 13 mitochondrial DNA protein coding genes ND6 may have evolved more rapidly and COIII was the most conserved. There are signs that ND6 may have been subjected to positive selection in order for these cichlid lineages to diversify and adapt to new environments. More work is needed to characterize the southern Africa cichlids as they are important species for capture fisheries, aquaculture development and understanding biogeographic history of African cichlids. Bio-conservation of some endangered cichlids is also essential due to the threat by invasive species.
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Affiliation(s)
- Ian Bbole
- Department of Fisheries, Mansa, Zambia
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Jin-Liang Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN), Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Shou-Jie Tang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Cyprian Katongo
- Biological Sciences Department, University of Zambia, Lusaka, Zambia
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16
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Turanov SV, Lee YH, Kartavtsev YP. Structure, evolution and phylogenetic informativeness of eelpouts (Cottoidei: Zoarcales) mitochondrial control region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:264-272. [PMID: 29991298 DOI: 10.1080/24701394.2018.1484117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales). To achieve this, we carried out a comparative phylogenetic and structural analysis of 29 CR sequences belonging to the long shanny Stichaeus grigorjewi together with nine sequences of other eelpouts taxa representing four families in contrast to mitochondrial protein-coding fragments. The CR organization within S. grigorjewi, as well as in all other eelpouts, is consistent with the common three-domain structure known from most vertebrates. We found a hidden CR variation constrains on the landscape level and a lack of nucleotide saturation. Finally, our results demonstrate the advantage of the length variation in CR sequences for phylogenetic reconstructions among eelpouts.
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Affiliation(s)
- Sergei V Turanov
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,b Chair of Water Biological Resources and Aquaculture, Far Eastern State Technical Fisheries University , Vladivostok , Russia
| | - Youn-Ho Lee
- c Laboratory of Marine Genomics, Korean Institute of Ocean Science and Technology , Ansan , Republic of Korea
| | - Yuri Ph Kartavtsev
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,d Chair of Biodiversity and Marine Bioresources, Far Eastern Federal University , Vladivostok , Russia
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17
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The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites. Sci Rep 2018; 8:7558. [PMID: 29765106 PMCID: PMC5954100 DOI: 10.1038/s41598-018-25981-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/02/2018] [Indexed: 01/06/2023] Open
Abstract
Bilaterian mitochondrial (mt) genomes are circular molecules that typically contain 37 genes. To date, only a single complete mitogenome sequence is available for the species-rich sarcoptiform mite order Oribatida. We sequenced the mitogenome of Paraleius leontonychus, another species of this suborder. It is 14,186 bp long and contains 35 genes, including only 20 tRNAs, lacking tRNAGly and tRNATyr. Re-annotation of the mitogenome of Steganacarus magnus increased the number of mt tRNAs for this species to 12. As typical for acariform mites, many tRNAs are highly truncated in both oribatid species. The total number of tRNAs and the number of tRNAs with a complete cloverleaf-like structure in P. leontonychus, however, clearly exceeds the numbers previously reported for Sarcoptiformes. This indicates, contrary to what has been previously assumed, that reduction of tRNAs is not a general characteristic for sarcoptiform mites. Compared to other Sarcoptiformes, the two oribatid species have the least rearranged mt genome with respect to the pattern observed in Limulus polyphemus, a basal arachnid species. Phylogenetic analysis of the newly sequenced mt genome and previously published data on other acariform mites confirms paraphyly of the Oribatida and an origin of the Astigmata within the Oribatida.
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Lin J, Adjeroh DA, Jiang BH, Jiang Y. K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics. Bioinformatics 2018; 34:1682-1689. [PMID: 29253072 PMCID: PMC6355110 DOI: 10.1093/bioinformatics/btx809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. Results We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. Availability and implementation The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). Contact yueljiang@163.com. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jie Lin
- Department of Software engineering, College of Mathematics and
Informatics, Fujian Normal University, Fuzhou, China
| | - Donald A Adjeroh
- Department of Computer Science & Electrical Engineering, West
Virginia University, Morgantown, WV, USA
| | - Bing-Hua Jiang
- Department of Pathology, Carver College of Medicine, The University of
Iowa, Iowa City, IA, USA
| | - Yue Jiang
- Department of Software engineering, College of Mathematics and
Informatics, Fujian Normal University, Fuzhou, China
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19
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Shi LX, Zhang C, Wang YP, Tang QY, Danley PD, Liu HZ. Evolutionary relationships of two balitorids (Cypriniformes, Balitoridae) revealed by comparative mitogenomics. ZOOL SCR 2018. [DOI: 10.1111/zsc.12282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Li-Xia Shi
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Chen Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Yin-Ping Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Qiong-Ying Tang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- College of Life Sciences; Huzhou University; Huzhou, Zhejiang China
| | | | - Huan-Zhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
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20
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Villela LCV, Alves AL, Varela ES, Yamagishi MEB, Giachetto PF, da Silva NMA, Ponzetto JM, Paiva SR, Caetano AR. Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree. Genetica 2017; 145:51-66. [DOI: 10.1007/s10709-016-9945-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/22/2016] [Indexed: 01/08/2023]
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21
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Künstner A, Hoffmann M, Fraser BA, Kottler VA, Sharma E, Weigel D, Dreyer C. The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population. PLoS One 2016; 11:e0169087. [PMID: 28033408 PMCID: PMC5199103 DOI: 10.1371/journal.pone.0169087] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/12/2016] [Indexed: 11/18/2022] Open
Abstract
For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (π) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.
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Affiliation(s)
- Axel Künstner
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Guest Group Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| | - Margarete Hoffmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Bonnie A. Fraser
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Verena A. Kottler
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eshita Sharma
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christine Dreyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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22
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Gao J, Zhao J. Complete mitochondrial genome of Copadichromis virginalis (Cichlidae). Mitochondrial DNA B Resour 2016; 1:152-153. [PMID: 33473442 PMCID: PMC7800849 DOI: 10.1080/23802359.2016.1144106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In this study, we report the complete mitochondrial genome of Copadichromis virginalis (Cichlidae fish). The mitochondrial genome is 16 704 bp in length and has a base composition of A (27.6%), T (30.1%), C (15.7%) and G (26.6%), demonstrating a slight bias of high AT content (57.6%). It contains 35 genes (13 protein-coding genes, 22 tRNAs and two rRNAs) and a non-coding A + T rich region (D-loop region). The mitochondial genome of Copadichromis virginalis presents a clear bias in nucleotied composition with a positive AT-skew and a negative GC-skew. Except for ND6 gene, all other protein-coding genes were located on the H-strand. ND4 gene and ND4L gene were overlapped by 5 bp, ATP8 gene and ATP6 gene were overlapped by 9 bp. The nucleotide sequence of 13 protein-coding genes of Copadichromis virginalis and other 19 Cichlidae species were used for phylogenetic analysis. The result indicated Copadichromis virginalis a close relationship with species Astatotilapia calliptera.
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Affiliation(s)
- Jian Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Jia Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
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23
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Zhao J, Gao J. Complete mitochondrial genome of Aulonocara stuartgranti (Flavescent peacock cichlid). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:279-280. [PMID: 26713354 DOI: 10.3109/19401736.2015.1118079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of the flavescent peacock cichlid Aulonocara stuartgranti was determined. The mitochondrial genome is 16 669 bp in length, and encodes 1 D-loop region, 2 ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. Average GC content of this genome is 45.8%. ATP8 and ATP6 genes overlap by nine nucleotides, ND5 and ND6 genes by four nucleotides, and ND4L and ND4 genes share six nucleotides. All coding genes use ATG as start codon with except COX1 initiating with GTG. The phylogenetic tree involving 22 available closely related species further validated the newly determined sequences and phylogeny of A. stuartgranti.
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Affiliation(s)
- Jia Zhao
- a BGI Education Center , University of Chinese Academy of Sciences , Shenzhen , China
| | - Jian Gao
- a BGI Education Center , University of Chinese Academy of Sciences , Shenzhen , China
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24
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Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations. Int J Mol Sci 2015; 16:25031-49. [PMID: 26492246 PMCID: PMC4632788 DOI: 10.3390/ijms161025031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 01/01/2023] Open
Abstract
To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.
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25
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Sahoo PK, Goel C, Kumar R, Dhama N, Ali S, Sarma D, Nanda P, Barat A. The complete mitochondrial genome of threatened chocolate mahseer (Neolissochilus hexagonolepis) and its phylogeny. Gene 2015; 570:299-303. [DOI: 10.1016/j.gene.2015.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 07/01/2015] [Accepted: 07/09/2015] [Indexed: 11/30/2022]
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26
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Kinaro ZO, Xue L, Volatiana JA. Complete mitochondrial DNA sequences of the Victoria tilapia (Oreochromis variabilis) and Redbelly Tilapia (Tilapia zilli): genome characterization and phylogeny analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2455-7. [PMID: 27158785 DOI: 10.3109/19401736.2015.1033695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Cichlid fishes have played an important role in evolutionary biology, population studies and aquaculture industry with East African species representing a model suited for studying adaptive radiation and speciation for cichlid genome projects in which closely related genomes are fast emerging presenting questions on phenotype-genotype relations. The complete mitochondrial genomes presented here are for two closely related but eco-morphologically distinct Lake Victoria basin cichlids, Oreochromis variabilis, an endangered native species and Tilapia zilli, an invasive species, both of which are important economic fishes in local areas. The complete mitochondrial genomes determined for O. variabilis and T. zilli are 16 626 and 16,619 bp, respectively. Both the mitogenomes contain 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a non-coding control region, which are typical of vertebrate mitogenomes. Phylogenetic analyses of the two species revealed that though both lie within family Cichlidae, they are remotely related.
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Affiliation(s)
- Zachary Omambia Kinaro
- a Department of Aquaculture , College of Marine Sciences, Ningbo University , Ningbo , Zhejiang , China .,b Directorate of Fisheries, Kisii County Government, Kisii , Kenya , and
| | - Liangyi Xue
- a Department of Aquaculture , College of Marine Sciences, Ningbo University , Ningbo , Zhejiang , China .,c Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University , Ningbo , Zhejiang , China
| | - Josies Ancella Volatiana
- a Department of Aquaculture , College of Marine Sciences, Ningbo University , Ningbo , Zhejiang , China
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27
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Mu X, Wang X, Liu Y, Song H, Liu C, Gu D, Wei H, Luo J, Hu Y. An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion. Gene 2015; 573:216-24. [PMID: 26187073 DOI: 10.1016/j.gene.2015.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
Flatfishes (Pleuronectiformes) exhibit different types of large-scale gene rearrangements. In the present study, the mitochondrial (mt) genome (18,369bp) of a tonguefish, Cynoglossus trigrammus, was determined using de novo mitochondrion genome sequencing. Compared with other flatfishes, the mt genome of C. trigrammus revealed distinct mitogenome architectures that primarily included two striking findings: 1) insertion of an additional long non-coding region (1647bp) making it the second largest genome length among Pleuronectiformes and 2) the translocation of the control region. The reconstructed phylogenetic tree based on 13 mt protein-coding gene sequences recovered the monophyletic suborder Pleuronectoidei and the family Cynoglossidae. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.
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Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xuejie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yi Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chao Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Dangen Gu
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hui Wei
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jianren Luo
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yinchang Hu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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28
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Liu L, He J, Li N, Fu X, Lin Q, Shi C, Lv Y, Zhang Z. Complete mitochondrial genome of Parachromis managuensis (Perciformes: Cichlidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2533-4. [PMID: 26153742 DOI: 10.3109/19401736.2015.1038791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Parachromis managuensis (Perciformes: Cichlidae) is sequenced in this study. The genome sequence was 16 526 bp in length, with the base composition of 28.1% A, 25.5% T, 15.4% G, 31.0% C. The gene order and genes are the same as found in other previously reported cichlid fish, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 D-loop region. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. Parachromis managuensis was closely related to Amphilophus citrinellus and Petenia splendid, based on its complete mitochondrial genome sequences. This complete mitogenome data provide the basis for taxonomic and conservation research of Parachromis managuensis.
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Affiliation(s)
- Lihui Liu
- a Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China .,b Key Laboratory of Fishery Drug Development , Ministry of Agriculture , Guangzhou , China .,c Key Laboratory of Aquatic Animal Immune Technology , Guangdong Provinces , Guangzhou , China , and
| | - Jinzhao He
- d Guangxi Aquatic Introducing and Breeding Center , Nanning , China
| | - Ningqiu Li
- a Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China .,b Key Laboratory of Fishery Drug Development , Ministry of Agriculture , Guangzhou , China .,c Key Laboratory of Aquatic Animal Immune Technology , Guangdong Provinces , Guangzhou , China , and
| | - Xiaozhe Fu
- a Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China .,b Key Laboratory of Fishery Drug Development , Ministry of Agriculture , Guangzhou , China .,c Key Laboratory of Aquatic Animal Immune Technology , Guangdong Provinces , Guangzhou , China , and
| | - Qiang Lin
- a Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China .,b Key Laboratory of Fishery Drug Development , Ministry of Agriculture , Guangzhou , China .,c Key Laboratory of Aquatic Animal Immune Technology , Guangdong Provinces , Guangzhou , China , and
| | - Cunbin Shi
- a Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China .,b Key Laboratory of Fishery Drug Development , Ministry of Agriculture , Guangzhou , China .,c Key Laboratory of Aquatic Animal Immune Technology , Guangdong Provinces , Guangzhou , China , and
| | - Yejian Lv
- d Guangxi Aquatic Introducing and Breeding Center , Nanning , China
| | - Zhixin Zhang
- d Guangxi Aquatic Introducing and Breeding Center , Nanning , China
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Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes. Meta Gene 2015; 5:105-14. [PMID: 26137446 PMCID: PMC4484717 DOI: 10.1016/j.mgene.2015.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/30/2015] [Accepted: 06/07/2015] [Indexed: 11/20/2022] Open
Abstract
Whole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequence the mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data of Clarias batrachus, generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome using both de novo and reference based approaches. Both the methods yielded almost similar results and the best assembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotation resulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order was found to be identical with other catfishes. Variation analyses between assembled and the reference (GenBank Acc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequences and tRNA supports the monophyly of catfishes. Two SSRs were identified in C. batrachus mitogenome, out of which one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrial genes were found to evolve at a much faster pace than the d-loop, which in turn are followed by the rRNAs; the tRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among the coding genes, ND2 evolves most rapidly. The variations present in the coding regions of the mitogenome and their comparative analyses with other catfish species may be useful in species conservation and management programs.
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Song HM, Liu C, Liu Y, Wei MX, Luo JR, Hu YC. Complete mitochondrial genome of the Red devil cichlid (Amphilophus citrinellus). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:840-1. [PMID: 24892490 DOI: 10.3109/19401736.2014.919467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome sequence of Amphilophus citrinellus was firstly sequenced and determined. The total genome is 16,522 bp in length with an A + T content of 54.19%, and contained 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and two main non-coding regions. The gene composition and order is similar to that of most other vertebrates, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Cichlidae species.
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Affiliation(s)
- Hong-Mei Song
- a Key Lab of Tropical and Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , PR China and
| | - Chao Liu
- a Key Lab of Tropical and Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , PR China and
| | - Yi Liu
- a Key Lab of Tropical and Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , PR China and
| | - Min-Xia Wei
- b College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , PR China
| | - Jian-ren Luo
- a Key Lab of Tropical and Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , PR China and
| | - Yin-chang Hu
- a Key Lab of Tropical and Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , PR China and
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Mu XD, Liu C, Wang XJ, Liu Y, Hu YC, Luo JR. Complete mitochondrial genome of Zebra tilapia, Tilapia buttikoferi. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:44-5. [PMID: 24438265 DOI: 10.3109/19401736.2013.869687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We determined the complete mitochondrial genome of Tilapia buttikoferi, which was 16,577 bp in length with an A + T content of 53.0%, containing 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a complete control region. The gene arrangement was similar to that of typical fishes. The total base composition of the mitogenome was 25.6% T, 30.8% C, 27.4% A and 16.2% G. Of the 13 protein-coding genes, 12 genes start with an ATG codon, except for COX1 with GTG. Seven (ND1, ND2, COX1, ATPase8, ATPase6, ND4L and ND6) used TAA or AGA as the termination codon, whereas six (COX2, COX3, ND3, ND4, ND5 and cyt b) had incomplete stop codon T. Its control region was atypical in being short at 861 bp, and contained TACAT motif and one microsatellite-like region (TA)7. This mitogenome sequence data may be useful for phylogenetic and systematic analyses within the family Cichlaidae.
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Affiliation(s)
- Xi-Dong Mu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Chao Liu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Xue-Jie Wang
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Yi Liu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Yin-Chang Hu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
| | - Jian-Ren Luo
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture , Guangzhou , China
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