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Rogers RL, Grizzard SL, Garner JT. Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve Megalonaias nervosa. Mol Biol Evol 2023; 40:7026026. [PMID: 36738170 PMCID: PMC9976758 DOI: 10.1093/molbev/msad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, harvesting, and changes in fish-host prevalence. Currently, over 70% of species in North America are threatened, endangered or extinct. To characterize the genetic response to recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase-sized regions that are nearly monomorphic across the population, signals of strong, recent selection reshaping diversity across 73 Mb total. These signatures of selection are greater than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable elements (TEs) appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
| | | | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
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2
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Mejia-Trujillo R, Smith CH. The male-type mitochondrial genome of the freshwater mussel Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019 (Bivalvia: Unionidae). Mitochondrial DNA B Resour 2022; 7:1854-1858. [PMID: 36325280 PMCID: PMC9621207 DOI: 10.1080/23802359.2022.2134750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The global decline of freshwater mussels emphasizes the need to establish genetic resources to better understand their biology, including a unique mitochondrial biology known as doubly uniparental inheritance. In this study, we present the complete male-type (M-type) mitochondrial genome of the freshwater mussel, Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019. The M-type mtDNA is approximately 16 kilobases and contains 22 tRNAs, two rRNAs, and 14 protein-coding genes, including a male-specific open reading frame. Read coverage revealed that M-type mtDNA was more abundant than female-type mtDNA in male gonadal tissue, with respect to a non-spawning male individual. Novel mitogenomes were resolved within previously described sex-specific monophyletic clades across the subfamily Ambleminae. The availability of high-quality nuclear and mitochondrial genomic data for P. streckersoni makes it a model for future research into the potential role of mtDNA in sex determination or sexual development in freshwater mussels.
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Affiliation(s)
| | - Chase H. Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA,CONTACT Chase H. Smith Department of Integrative Biology, University of Texas, Austin, TX, USA
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3
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Lubośny M, Śmietanka B, Arculeo M, Burzyński A. No evidence of DUI in the Mediterranean alien species Brachidontes pharaonis (P. Fisher, 1870) despite mitochondrial heteroplasmy. Sci Rep 2022; 12:8569. [PMID: 35595866 PMCID: PMC9122905 DOI: 10.1038/s41598-022-12606-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 01/05/2023] Open
Abstract
Two genetically different mitochondrial haplogroups of Brachidontes pharaonis (p-distance 6.8%) have been identified in the Mediterranean Sea. This hinted at a possible presence of doubly uniparental inheritance in this species. To ascertain this possibility, we sequenced two complete mitogenomes of Brachidontes pharaonis mussels and performed a qPCR analysis to measure the relative mitogenome copy numbers of both mtDNAs. Despite the presence of two very similar regions composed entirely of repetitive sequences in the two haplogroups, no recombination between mitogenomes was detected. In heteroplasmic individuals, both mitogenomes were present in the generative tissues of both sexes, which argues against the presence of doubly uniparental inheritance in this species.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marco Arculeo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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4
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Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved. Sci Rep 2021; 11:13552. [PMID: 34193932 PMCID: PMC8245539 DOI: 10.1038/s41598-021-92994-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 12/15/2022] Open
Abstract
Contrary to the early evidence, which indicated that the mitochondrial architecture in one of the two major annelida clades, Sedentaria, is relatively conserved, a handful of relatively recent studies found evidence that some species exhibit elevated rates of mitochondrial architecture evolution. We sequenced complete mitogenomes belonging to two congeneric shell-boring Spionidae species that cause considerable economic losses in the commercial marine mollusk aquaculture: Polydora brevipalpa and Polydora websteri. The two mitogenomes exhibited very similar architecture. In comparison to other sedentarians, they exhibited some standard features, including all genes encoded on the same strand, uncommon but not unique duplicated trnM gene, as well as a number of unique features. Their comparatively large size (17,673 bp) can be attributed to four non-coding regions larger than 500 bp. We identified an unusually large (putative) overlap of 14 bases between nad2 and cox1 genes in both species. Importantly, the two species exhibited completely rearranged gene orders in comparison to all other available mitogenomes. Along with Serpulidae and Sabellidae, Polydora is the third identified sedentarian lineage that exhibits disproportionally elevated rates of mitogenomic architecture rearrangements. Selection analyses indicate that these three lineages also exhibited relaxed purifying selection pressures.
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5
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Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021; 13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
- Biology Department, Baylor University, Waco, Texas, USA
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6
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Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, Garner JT, Moore CC. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol 2021; 30:1155-1173. [PMID: 33382161 DOI: 10.1111/mec.15786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways and overfishing. These species are notable for their unusual life history strategy, parasite-host co-evolution and biparental mitochondrial inheritance. Among this clade, the washboard mussel Megalonaias nervosa is one species that remains prevalent across the Southeastern United States, with robust population sizes. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe dynamic changes in genome content, with a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Birth-death models suggest rapid expansions among gene families, with a mutation rate of 1.16 × 10-8 duplications per gene per generation. Cytochrome P450 gene families have experienced exceptional recent amplification beyond expectations based on genome-wide birth-death processes. These genes are associated with increased rates of amino acid changes, a signature of selection driving evolution of detox genes. Fitting evolutionary models of adaptation from standing genetic variation, we can compare adaptive potential across species and mutation types. The large population size in M. nervosa suggests a 4.7-fold advantage in the ability to adapt from standing genetic variation compared with a low diversity endemic E. hopetonensis. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv = 0.185 compared with Psgv = 0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of 'hopeful monsters' within the genome that may facilitate adaptation when selective pressures shift. These results suggest that gene family expansion is a key driver of adaptive evolution in this key species of freshwater Unionidae that is currently facing widespread environmental challenges. This work has clear implications for conservation genomics on freshwater bivalves as well as evolutionary theory. This genome represents a first step to facilitate reverse ecological genomics in Unionidae and identify the genetic underpinnings of phenotypic diversity.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | - Stephanie L Grizzard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | | | - Katherine Bockrath
- Department of Genetics, University of Georgia, Athens, GA, USA.,U.S. Fish and Wildlife Service, Midwest Fisheries Center Whitney Genetics Lab, Onalaska, WI, USA
| | - Sagar Patel
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - John P Wares
- Department of Genetics, University of Georgia, Athens, GA, USA.,Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
| | - Cathy C Moore
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
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7
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Wu RW, Liu XJ, Ouyang S, Wu XP. Comparative Analyses of the Complete Mitochondrial Genomes of Three Lamprotula (Bivalvia: Unionidae) Species: Insight into the Shortcomings of Mitochondrial DNA for Recently Diverged Species Delimitation. MALACOLOGIA 2020. [DOI: 10.4002/040.063.0106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Rui-Wen Wu
- School of Life Sciences, Nanchang University, Nanchang 330031, People's Republic of China
| | - Xiong-Jun Liu
- School of Resource, Environment and Chemical Engineering, Nanchang University, Nanchang 330031, People's Republic of China
| | - Shan Ouyang
- School of Life Sciences, Nanchang University, Nanchang 330031, People's Republic of China
| | - Xiao-Ping Wu
- School of Life Sciences, Nanchang University, Nanchang 330031, People's Republic of China
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8
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Morphology of Mitochondria in Syncytial Annelid Female Germ-Line Cyst Visualized by Serial Block-Face SEM. Int J Cell Biol 2020; 2020:7483467. [PMID: 32395131 PMCID: PMC7199535 DOI: 10.1155/2020/7483467] [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: 04/17/2019] [Revised: 07/11/2019] [Accepted: 08/04/2019] [Indexed: 11/23/2022] Open
Abstract
Mitochondria change their morphology and distribution depending on the metabolism and functional state of a cell. Here, we analyzed the mitochondria and selected structures in female germ-line cysts in a representative of clitellate annelids – the white worm Enchytraeus albidus in which each germ cell has one cytoplasmic bridge that connects it to a common cytoplasmic mass. Using serial block-face scanning electron microscopy (SBEM), we prepared three-dimensional ultrastructural reconstructions of the entire selected compartments of a cyst at the advanced stage of oogenesis, i.e. the nurse cell, cytophore, and cytoplasmic bridges of all 16 cells (15 nurse cells and oocyte). We revealed extensive mitochondrial networks in the nurse cells, cytophore and mitochondria that pass through the cytoplasmic bridges, which indicates that a mitochondrial network can extend throughout the entire cyst. The dynamic hyperfusion state was suggested for such mitochondrial aggregations. We measured the mitochondria distribution and revealed their polarized distribution in the nurse cells and more abundant accumulation within the cytophore compared to the nurse cell. A close association of mitochondrial networks with dispersed nuage material, which seems to be the structural equivalent of a Balbiani body, not described in clitellate annelids so far, was also revealed.
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9
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Wu RW, Liu XJ, Wang S, Roe KJ, Ouyang S, Wu XP. Analysis of mitochondrial genomes resolves the phylogenetic position of Chinese freshwater mussels (Bivalvia, Unionidae). Zookeys 2019; 812:23-46. [PMID: 30636909 PMCID: PMC6328525 DOI: 10.3897/zookeys.812.29908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Abstract
The Yangtze River basin is one of the most species-rich regions for freshwater mussels on Earth, but is gravely threatened by anthropogenic activities. However, conservation planning and management of mussel species has been hindered by a number of taxonomic uncertainties. In order to clarify the taxonomic status and phylogenetic position of these species, mitochondrial genomes of four species (Acuticostachinensis, Schistodesmuslampreyanus, Cuneopsisheudei and Cuneopsiscapitatus) were generated and analyzed along with data from 43 other mitogenomes. The complete F-type mitogenomes of A.chinensis, S.lampreyanus, C.heudei, and C.capitatus are 15652 bp, 15855 bp, 15892 bp, and 15844 bp, respectively, and all four F-type mitogenomes have the same pattern of gene arrangement. ML and BI trees based on the mitogenome dataset are completely congruent, and indicate that the included Unionidae belong to three subfamilies with high bootstrap and posterior probabilities, i.e., Unioninae (Aculamprotula, Cuneopsis, Nodularia, and Schistodesmus), Anodontinae (Cristaria, Arconaia, Acuticosta, Lanceolaria, Anemina, and Sinoanodonta), and Gonideinae (Ptychorhynchus, Solenaia, Lamprotula, and Sinohyriopsis). Results also indicate that A.chinensis has affinities with Arconaialanceolata and Lanceolariagrayii and is a member of the subfamily Anodontinae.
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Affiliation(s)
- Rui-Wen Wu
- School of Life Sciences, Nanchang University, Honggutan-New-District, Nanchang 330031, ChinaNanchang UniversityNanchangChina
| | - Xiong-Jun Liu
- School of Resource, Environment and Chemical Engineering, Nanchang University, Nanchang 330031, ChinaIowa State UniversityAmesUnited States of America
- Poyang Lake Key Laboratory of Environment and Resource Utilization (Nanchang University), Ministry of Education, Nanchang 330031, ChinaNanchang UniversityNanchangChina
| | - Sa Wang
- School of Life Sciences, Nanchang University, Honggutan-New-District, Nanchang 330031, ChinaNanchang UniversityNanchangChina
| | - Kevin J. Roe
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, 50011, United States of AmericaIowa State UniversityAmesUnited States of America
| | - Shan Ouyang
- School of Life Sciences, Nanchang University, Honggutan-New-District, Nanchang 330031, ChinaNanchang UniversityNanchangChina
| | - Xiao-Ping Wu
- School of Life Sciences, Nanchang University, Honggutan-New-District, Nanchang 330031, ChinaNanchang UniversityNanchangChina
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10
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Burzyński A, Soroka M. Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae). PeerJ 2018; 6:e5573. [PMID: 30221094 PMCID: PMC6138038 DOI: 10.7717/peerj.5573] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.
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Affiliation(s)
- Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marianna Soroka
- University of Szczecin, Faculty of Biology, Department of Genetics, Szczecin, Poland
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11
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Liu ZQ, Liu YF, Kuermanali N, Wang DF, Chen SJ, Guo HL, Zhao L, Wang JW, Han T, Wang YZ, Wang J, Shen CF, Zhang ZZ, Chen CF. Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae. PLoS One 2018; 13:e0197524. [PMID: 29768482 PMCID: PMC5955544 DOI: 10.1371/journal.pone.0197524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/03/2018] [Indexed: 02/07/2023] Open
Abstract
Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1. sequence the first Hyalomma mitogenome; 2. scrutinise the proposed synonymization using molecular data, i.e. complete mitogenomes of both subspecies: H. a. asiaticum and kozlovi; 3. conduct phylogenomic and comparative analyses of all available Ixodidae mitogenomes. Results corroborate the proposed synonymization: the two mitogenomes are almost identical (99.6%). Genomic features of both mitogenomes are standard for Metastriata; which includes the presence of two control regions and all three "Tick-Box" motifs. Gene order and strand distribution are perfectly conserved for the entire Metastriata group. Suspecting compositional biases, we conducted phylogenetic analyses (29 almost complete mitogenomes) using homogeneous and heterogeneous (CAT) models of substitution. The results were congruent, apart from the deep-level topology of prostriate ticks (Ixodes): the homogeneous model produced a monophyletic Ixodes, but the CAT model produced a paraphyletic Ixodes (and thereby Prostriata), divided into Australasian and non-Australasian clades. This topology implies that all metastriate ticks have evolved from the ancestor of the non-Australian branch of prostriate ticks. Metastriata was divided into three clades: 1. Amblyomminae and Rhipicephalinae (Rhipicephalus, Hyalomma, Dermacentor); 2. Haemaphysalinae and Bothriocrotoninae, plus Amblyomma sphenodonti; 3. Amblyomma elaphense, basal to all Metastriata. We conclude that mitogenomes have the potential to resolve the long-standing debate about the evolutionary history of ticks, but heterogeneous evolutionary models should be used to alleviate the effects of compositional heterogeneity on deep-level relationships.
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Affiliation(s)
- Zhi-Qiang Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Yan-Feng Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| | - Nuer Kuermanali
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Deng-Feng Wang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Shi-Jun Chen
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Hui-Ling Guo
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Li Zhao
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Jun-Wei Wang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Tao Han
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Yuan-Zhi Wang
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| | - Jie Wang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Chen-Feng Shen
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Zhuang-Zhi Zhang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Chuang-Fu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
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12
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Chase EE, Robicheau BM, Veinot S, Breton S, Stewart DT. The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida. BMC Genomics 2018; 19:221. [PMID: 29587633 PMCID: PMC5870820 DOI: 10.1186/s12864-018-4583-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/07/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Doubly uniparental inheritance (DUI) of mitochondrial DNA in bivalves is a fascinating exception to strictly maternal inheritance as practiced by all other animals. Recent work on DUI suggests that there may be unique regions of the mitochondrial genomes that play a role in sex determination and/or sexual development in freshwater mussels (order Unionoida). In this study, one complete mitochondrial genome of the hermaphroditic swan mussel, Anodonta cygnea, is sequenced and compared to the complete mitochondrial genome of the gonochoric duck mussel, Anodonta anatina. An in silico assessment of novel proteins found within freshwater bivalve species (known as F-, H-, and M-open reading frames or ORFs) is conducted, with special attention to putative transmembrane domains (TMs), signal peptides (SPs), signal cleavage sites (SCS), subcellular localization, and potential control regions. Characteristics of TMs are also examined across freshwater mussel lineages. RESULTS In silico analyses suggests the presence of SPs and SCSs and provides some insight into possible function(s) of these novel ORFs. The assessed confidence in these structures and functions was highly variable, possibly due to the novelty of these proteins. The number and topology of putative TMs appear to be maintained among both F- and H-ORFs, however, this is not the case for M-ORFs. There does not appear to be a typical control region in H-type mitochondrial DNA, especially given the loss of tandem repeats in unassigned regions when compared to F-type mtDNA. CONCLUSION In silico analyses provides a useful tool to discover patterns in DUI and to navigate further in situ analyses related to DUI in freshwater mussels. In situ analysis will be necessary to further explore the intracellular localizations and possible role of these open reading frames in the process of sex determination in freshwater mussel.
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Affiliation(s)
- E. E. Chase
- Department of Biology, Acadia University, Wolfville, NS Canada
| | - B. M. Robicheau
- Department of Biology, Dalhousie University, Halifax, NS Canada
| | - S. Veinot
- Department of Biology, Dalhousie University, Halifax, NS Canada
| | - S. Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - D. T. Stewart
- Department of Biology, Acadia University, Wolfville, NS Canada
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13
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Zou H, Jakovlić I, Chen R, Zhang D, Zhang J, Li WX, Wang GT. The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class. BMC Genomics 2017; 18:840. [PMID: 29096600 PMCID: PMC5669012 DOI: 10.1186/s12864-017-4237-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes. RESULTS The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder. CONCLUSIONS Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.
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Affiliation(s)
- Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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Liu ZQ, Kuermanali N, Li Z, Chen SJ, Wang YZ, Tao H, Chen CF. The complete mitochondrial genome of the parasitic sheep ked Melophagus ovinus (Diptera: Hippoboscidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:432-434. [PMID: 33473852 PMCID: PMC7800015 DOI: 10.1080/23802359.2017.1347832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complete mitochondrial genome (15,573 bp) of an understudied sheep parasite Melophagus ovinus was sequenced and characterized. Its organization and characteristics, including the size, structure, gene order, start/stop codon usage and gene overlaps, are largely typical for Diptera. It exhibits very high A + T bias (81%). Posterior probability values in the inferred phylogenetic dendrogram were very high, but Oestroidea and Muscoidea superfamilies were both paraphyletic. The sequence was nested within the Oestridae clade, thus also rendering the family paraphyletic. A larger number of Hippoboscoidea mitogenomes will have to be available to achieve a better phylogenetic resolution.
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Affiliation(s)
- Zhi-Qiang Liu
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China.,College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| | - Nuer Kuermanali
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Zhao Li
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Shi-Jun Chen
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yuan-Zhi Wang
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| | - Han Tao
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Chuang-Fu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
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