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Li N, Flanagan BA, Edmands S. The role of mitochondria in sex- and age-specific gene expression in a species without sex chromosomes. Proc Natl Acad Sci U S A 2024; 121:e2321267121. [PMID: 38838014 PMCID: PMC11181141 DOI: 10.1073/pnas.2321267121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Mitochondria perform an array of functions, many of which involve interactions with gene products encoded by the nucleus. These mitochondrial functions, particularly those involving energy production, can be expected to differ between sexes and across ages. Here, we measured mitochondrial effects on sex- and age-specific gene expression in parental and reciprocal F1 hybrids between allopatric populations of Tigriopus californicus with over 20% mitochondrial DNA divergence. Because the species lacks sex chromosomes, sex-biased mitochondrial effects are not confounded by the effects of sex chromosomes. Results revealed pervasive sex differences in mitochondrial effects, including effects on energetics and aging involving nuclear interactions throughout the genome. Using single-individual RNA sequencing, sex differences were found to explain more than 80% of the variance in gene expression. Males had higher expression of mitochondrial genes and mitochondrially targeted proteins (MTPs) involved in oxidative phosphorylation (OXPHOS), while females had elevated expression of non-OXPHOS MTPs, indicating strongly sex-dimorphic energy metabolism at the whole organism level. Comparison of reciprocal F1 hybrids allowed insights into the nature of mito-nuclear interactions, showing both mitochondrial effects on nuclear expression, and nuclear effects on mitochondrial expression. While based on a small set of crosses, sex-specific increases in mitochondrial expression with age were associated with longer life. Network analyses identified nuclear components of strong mito-nuclear interactions and found them to be sexually dimorphic. These results highlight the profound impact of mitochondria and mito-nuclear interactions on sex- and age-specific gene expression.
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Affiliation(s)
- Ning Li
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90089
| | - Ben A. Flanagan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90089
| | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90089
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2
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Li N, Flanagan BA, Edmands S. The role of mitochondria in sex- and age-specific gene expression in a species without sex chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570893. [PMID: 38106076 PMCID: PMC10723445 DOI: 10.1101/2023.12.08.570893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mitochondria perform an array of functions, many of which involve interactions with gene products encoded by the nucleus. These mitochondrial functions, particularly those involving energy production, can be expected to differ between sexes and across ages. Here we measured mitochondrial effects on sex- and age-specific gene expression in parental and reciprocal F1 hybrids between allopatric populations of Tigriopus californicus with over 20% mitochondrial DNA divergence. Because the species lacks sex chromosomes, sex-biased mitochondrial effects are not confounded by the effects of sex chromosomes. Using single-individual RNA sequencing, sex differences were found to explain more than 80% of the variance in gene expression. Males had higher expression of mitochondrial genes and mitochondrially targeted proteins (MTPs) involved in oxidative phosphorylation (OXPHOS), while females had elevated expression of non-OXPHOS MTPs, indicating strongly sex-dimorphic energy metabolism at the whole organism level. Comparison of reciprocal F1 hybrids allowed insights into the nature of mito-nuclear interactions, showing both mitochondrial effects on nuclear expression, as well as nuclear effects on mitochondrial expression. Across both sexes, increases in mitochondrial expression with age were associated with longer life. Network analyses identified nuclear components of strong mito-nuclear interactions, and found them to be sexually dimorphic. These results highlight the profound impact of mitochondria and mito-nuclear interactions on sex- and age-specific gene expression.
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Affiliation(s)
- Ning Li
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | | | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
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3
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Kayhani K, Barreto FS. Disproportionate role of nuclear-encoded proteins in organismal and mitochondrial thermal performance in a copepod. J Exp Biol 2023; 226:jeb246085. [PMID: 37947077 DOI: 10.1242/jeb.246085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
Determining the mechanisms by which organisms evolve thermal tolerance is crucial to predicting how populations may respond to changes in local temperature regimes. Although evidence of relationships between mitochondrial background and thermal adaptation have been found, the presence of both nuclear-encoded and mitochondrial DNA (mtDNA)-encoded proteins warrants experiments aimed at parsing out the relative role of each genome in thermal adaptation. We investigated the relative role of mtDNA-encoded products in thermal tolerance between two divergent populations of Tigriopus californicus using first-generation (F1) hybrids that vary in maternally inherited mtDNA but are heterozygous for population-specific alleles across nuclear loci. We tested two measures of thermal tolerance, (1) survivorship to acute thermal stress and (2) thermal stability of mitochondrial performance in Complex I-fueled ATP synthesis, both across a range of increasing temperatures. We found that the southern population (San Diego, CA, USA) outperformed the northern population (Strawberry Hill, OR, USA) in survivorship, and that both reciprocal F1 hybrid crosses had intermediate survival. Mitochondria from the San Diego population displayed greater stability in ATP synthesis with increasing temperatures compared with those from Strawberry Hill. Interestingly, hybrids from both cross directions had synthesis profiles that were very similar to that of Strawberry Hill. Taken together, these results suggest that the relative role of the mtDNA in these phenotypes is negligible compared with that of elements encoded by nuclear DNA in this system.
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Affiliation(s)
- Kamron Kayhani
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Felipe S Barreto
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
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4
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Ignatavičienė I, Ragauskas A, Rakauskas V, Butkauskas D. Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus. Biol Methods Protoc 2023; 8:bpad022. [PMID: 37817807 PMCID: PMC10561993 DOI: 10.1093/biomethods/bpad022] [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: 07/19/2023] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
Studies on genetic diversity require biological material containing a reliable source of DNA that can be extracted and analyzed. Recently, non-invasive sampling has become a preferred sampling method of biological material. The suitability of a less invasive approach that involves obtaining samples by swabbing the fish skin (including live, non-anesthetized fish) should be considered. In this study, we compared the efficiency of DNA extraction, amplification, and sequencing of mtDNA fragments of two fish species Perca fluviatilis and Rutilus rutilus based on DNA collected from the scales and mucus using the modified Aljanabi and Martinez method. The results revealed a higher quality of DNA extracted from the mucus; however, the mean DNA concentration obtained from the scales of both fish species was higher. We verified the method suitable for amplification and sequencing of mtDNA fragments of both fish species using newly designed markers (D-loop, ATP6) and examined the potential risk of intraspecific cross-contamination. The DNA sequence alignment analysis revealed identical sequences attributed to the same individual when DNA, extracted from two different sources (scales and mucus), was used. We demonstrated that the quantity and quality of DNA extracted from the scales and mucus using the proposed method were high enough to carry out genetic diversity studies based on sampling of live fish with the possibility to release it after collecting samples.
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5
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Healy TM, Burton RS. Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence. Evolution 2023; 77:2100-2108. [PMID: 37407024 DOI: 10.1093/evolut/qpad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.
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Affiliation(s)
- Timothy M Healy
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
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6
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Deconinck A, Willett CS. Hypoxia tolerance, but not low pH tolerance, is associated with a latitudinal cline across populations of Tigriopus californicus. PLoS One 2022; 17:e0276635. [PMID: 36301968 PMCID: PMC9612455 DOI: 10.1371/journal.pone.0276635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Intertidal organisms must tolerate daily fluctuations in environmental parameters, and repeated exposure to co-occurring conditions may result in tolerance to multiple stressors correlating. The intertidal copepod Tigriopus californicus experiences diurnal variation in dissolved oxygen levels and pH as the opposing processes of photosynthesis and cellular respiration lead to coordinated highs during the day and lows at night. While environmental parameters with overlapping spatial gradients frequently result in correlated traits, less attention has been given to exploring temporally correlated stressors. We investigated whether hypoxia tolerance correlates with low pH tolerance by separately testing the hypoxia and low pH stress tolerance separately of 6 genetically differentiated populations of T. californicus. We independently checked for similarities in tolerance for each of the two stressors by latitude, sex, size, and time since collection as predictors. We found that although hypoxia tolerance correlated with latitude, low pH tolerance did not, and no predictor was significant for both stressors. We concluded that temporally coordinated exposure to low pH and low oxygen did not result in populations developing equivalent tolerance for both. Although climate change alters several environmental variables simultaneously, organisms' abilities to tolerate these changes may not be similarly coupled.
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Affiliation(s)
- Aimee Deconinck
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Christopher S. Willett
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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David P, Degletagne C, Saclier N, Jennan A, Jarne P, Plénet S, Konecny L, François C, Guéguen L, Garcia N, Lefébure T, Luquet E. Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination. Curr Biol 2022; 32:2325-2333.e6. [PMID: 35483362 DOI: 10.1016/j.cub.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/06/2022] [Indexed: 01/06/2023]
Abstract
Cytoplasmic male sterility (CMS) is a form of genetic conflict over sex determination that results from differences in modes of inheritance between genomic compartments.1-3 Indeed, maternally transmitted (usually mitochondrial) genes sometimes enhance their transmission by suppressing the male function in a hermaphroditic organism to the detriment of biparentally inherited nuclear genes. Therefore, these hermaphrodites become functionally female and may coexist with regular hermaphrodites in so-called gynodioecious populations.3 CMS has been known in plants since Darwin's times4 but is previously unknown in the animal kingdom.5-8 We relate the first observation of CMS in animals. It occurs in a freshwater snail population, where some individuals appear unable to sire offspring in controlled crosses and show anatomical, physiological, and behavioral characters consistent with a suppression of the male function. Male sterility is associated with a mitochondrial lineage that underwent a spectacular acceleration of DNA substitution rates, affecting the entire mitochondrial genome-this acceleration concerns both synonymous and non-synonymous substitutions and therefore results from increased mitogenome mutation rates. Consequently, mitochondrial haplotype divergence within the population is exceptionally high, matching that observed between snail taxa that diverged 475 million years ago. This result is reminiscent of similar accelerations in mitogenome evolution observed in plant clades where gynodioecy is frequent,9,10 both being consistent with arms-race evolution of genome regions implicated in CMS.11,12 Our study shows that genomic conflicts can trigger independent evolution of similar sex-determination systems in plants and animals and dramatically accelerate molecular evolution.
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Affiliation(s)
- Patrice David
- CEFE, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France.
| | - Cyril Degletagne
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | | | - Aurel Jennan
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Philippe Jarne
- CEFE, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France
| | - Sandrine Plénet
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Lara Konecny
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | | | - Laurent Guéguen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Noéline Garcia
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Tristan Lefébure
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Emilien Luquet
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
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8
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Lee J, Willett CS. Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids. J Hered 2022; 113:171-183. [PMID: 35575078 DOI: 10.1093/jhered/esab068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.
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Affiliation(s)
- Jeeyun Lee
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher S Willett
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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9
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Zhang B, Havird JC, Wang E, Lv J, Xu X. Massive gene rearrangement in mitogenomes of phytoseiid mites. Int J Biol Macromol 2021; 186:33-39. [PMID: 34237359 DOI: 10.1016/j.ijbiomac.2021.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 01/14/2023]
Abstract
Mitochondrial (mt) gene sequences have been widely used to infer phylogeny in animals. The relative order of mt genes in the mitogenome can also be a useful marker for evolution, but the propensity of mt gene rearrangements vary tremendously among taxa. Ticks and mites in Acari exemplify this trend as some families retain the ancestral arthropod gene order, while others show highly divergent gene orders. Mites in Phytoseiidae, many of which are effective biological control agents, show some of the most divergent gene orders. However, the diversity of mitogenome order within this family is little known. We thus sequenced three mt genomes of phytoseiid mites from two of the most speciose genera: Amblyseius swirskii (Athias-Henriot), Amblyseius tsugawai (Ehara) and Neoseiulus womersleyi (Schicha). We find differences in mt GC skew and nucleotide composition, especially between N. womersleyi and the two Amblyseius species. Each species within Phytoseiidae (including three previously available sequences) present a unique gene order. Phytoseiid mitogenomes show some of the highest numbers of breakpoints when compared to the ancestral arthropod order (up to 33), as well as high numbers of breakpoints within the family (14-30). This suggests a history of massive, ongoing mitogenome rearrangements in the family. Phylogenetic analyses of mt sequences confirm that the degree of gene rearrangements follows phylogenetic relatedness. We discuss possible causes for the high degree of mt gene rearrangement within phytoseiid mites as well as selection in the mt and nuclear genome tied to the independent evolution of many diverse feeding strategies in the family. Finally, we suggest N. womersleyi should be used instead of the synonym Amblyseius pseudolongispinosus.
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Affiliation(s)
- Bo Zhang
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Endong Wang
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jiale Lv
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xuenong Xu
- Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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Han KL, Barreto FS. Pervasive Mitonuclear Coadaptation Underlies Fast Development in Interpopulation Hybrids of a Marine Crustacean. Genome Biol Evol 2021; 13:6121088. [PMID: 33502469 PMCID: PMC7947751 DOI: 10.1093/gbe/evab004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/21/2022] Open
Abstract
Cellular energy production requires coordinated interactions between genetic components from the nuclear and mitochondrial genomes. This coordination results in coadaptation of interacting elements within populations. Interbreeding between divergent gene pools can disrupt coadapted loci and result in hybrid fitness breakdown. While specific incompatible loci have been detected in multiple eukaryotic taxa, the extent of the nuclear genome that is influenced by mitonuclear coadaptation is not clear in any species. Here, we used F2 hybrids between two divergent populations of the copepod Tigriopus californicus to examine mitonuclear coadaptation across the nuclear genome. Using developmental rate as a measure of fitness, we found that fast-developing copepods had higher ATP synthesis capacity than slow developers, suggesting variation in developmental rates is at least partly associated with mitochondrial dysfunction. Using Pool-seq, we detected strong biases for maternal alleles across 7 (of 12) chromosomes in both reciprocal crosses in high-fitness hybrids, whereas low-fitness hybrids showed shifts toward the paternal population. Comparison with previous results on a different hybrid cross revealed largely different patterns of strong mitonuclear coadaptation associated with developmental rate. Our findings suggest that functional coadaptation between interacting nuclear and mitochondrial components is reflected in strong polygenic effects on this life-history phenotype, and reveal that molecular coadaptation follows independent evolutionary trajectories among isolated populations.
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Affiliation(s)
- Kin-Lan Han
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA.,Department of Biology, University of Washington, Seattle, Washington, USA
| | - Felipe S Barreto
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
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11
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Milani L, Ghiselli F. Faraway, so close. The comparative method and the potential of non-model animals in mitochondrial research. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190186. [PMID: 31787048 DOI: 10.1098/rstb.2019.0186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inference from model organisms has been the engine for many discoveries in life science, but indiscriminate generalization leads to oversimplifications and misconceptions. Model organisms and inductive reasoning are irreplaceable: there is no other way to tackle the complexity of living systems. At the same time, it is not advisable to infer general patterns from a restricted number of species, which are very far from being representative of the diversity of life. Not all models are equal. Some organisms are suitable to find similarities across species, other highly specialized organisms can be used to focus on differences. In this opinion piece, we discuss the dominance of the mechanistic/reductionist approach in life sciences and make a case for an enhanced application of the comparative approach to study processes in all their various forms across different organisms. We also enlist some rising animal models in mitochondrial research, to exemplify how non-model organisms can be chosen in a comparative framework. These taxa often do not possess implemented tools and dedicated methods/resources. However, because of specific features, they have the potential to address still unanswered biological questions. Finally, we discuss future perspectives and caveats of the comparative method in the age of 'big data'. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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12
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Healy TM, Bock AK, Burton RS. Variation in developmental temperature alters adulthood plasticity of thermal tolerance in Tigriopus californicus. ACTA ACUST UNITED AC 2019; 222:jeb.213405. [PMID: 31597734 DOI: 10.1242/jeb.213405] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022]
Abstract
In response to environmental change, organisms rely on both genetic adaptation and phenotypic plasticity to adjust key traits that are necessary for survival and reproduction. Given the accelerating rate of climate change, plasticity may be particularly important. For organisms in warming aquatic habitats, upper thermal tolerance is likely to be a key trait, and many organisms express plasticity in this trait in response to developmental or adulthood temperatures. Although plasticity at one life stage may influence plasticity at another life stage, relatively little is known about this possibility for thermal tolerance. Here, we used locally adapted populations of the copepod Tigriopus californicus to investigate these potential effects in an intertidal ectotherm. We found that low latitude populations had greater critical thermal maxima (CTmax) than high latitude populations, and variation in developmental temperature altered CTmax plasticity in adults. After development at 25°C, CTmax was plastic in adults, whereas no adulthood plasticity in this trait was observed after development at 20°C. This pattern was identical across four populations, suggesting that local thermal adaptation has not shaped this effect among these populations. Differences in the capacities to maintain ATP synthesis rates and to induce heat shock proteins at high temperatures, two likely mechanisms of local adaptation in this species, were consistent with changes in CTmax owing to phenotypic plasticity, which suggests that there is likely mechanistic overlap between the effects of plasticity and adaptation. Together, these results indicate that developmental effects may have substantial impacts on upper thermal tolerance plasticity in adult ectotherms.
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Affiliation(s)
- Timothy M Healy
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive #0202, La Jolla, CA 92093-0202, USA
| | - Antonia K Bock
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive #0202, La Jolla, CA 92093-0202, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive #0202, La Jolla, CA 92093-0202, USA
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13
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Hwang DS, Choi BS, Lee MC, Han J, Kim S, Lee JS. Complete mitochondrial genome of the Antarctic copepod Tigriopus kingsejongenesis (Harpacticoida, Harpacticidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2019.1601042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Dae-Sik Hwang
- Research Institute of Environmental Health and Safety, Bucheon, South Korea
| | | | - Min-Chul Lee
- Research Institute of Environmental Health and Safety, Bucheon, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Sanghee Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
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14
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Pichaud N, Bérubé R, Côté G, Belzile C, Dufresne F, Morrow G, Tanguay RM, Rand DM, Blier PU. Age Dependent Dysfunction of Mitochondrial and ROS Metabolism Induced by Mitonuclear Mismatch. Front Genet 2019; 10:130. [PMID: 30842791 PMCID: PMC6391849 DOI: 10.3389/fgene.2019.00130] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 02/06/2019] [Indexed: 12/26/2022] Open
Abstract
Mitochondrial and nuclear genomes have to coevolve to ensure the proper functioning of the different mitochondrial complexes that are assembled from peptides encoded by both genomes. Mismatch between these genomes is believed to be strongly selected against due to the consequent impairments of mitochondrial functions and induction of oxidative stress. Here, we used a Drosophila model harboring an incompatibility between a mitochondrial tRNAtyr and its nuclear-encoded mitochondrial tyrosine synthetase to assess the cellular mechanisms affected by this incompatibility and to test the relative contribution of mitonuclear interactions and aging on the expression of impaired phenotypes. Our results show that the mitochondrial tRNA mutation caused a decrease in mitochondrial oxygen consumption in the incompatible nuclear background but no effect with the compatible nuclear background. Mitochondrial DNA copy number increased in the incompatible genotype but that increase failed to rescue mitochondrial functions. The flies harboring mismatch between nuclear and mitochondrial genomes had almost three times the relative mtDNA copy number and fifty percent higher rate of hydrogen peroxide production compared to other genome combinations at 25 days of age. We also found that aging exacerbated the mitochondrial dysfunctions. Our results reveal the tight interactions linking mitonuclear mismatch to mitochondrial dysfunction, mitochondrial DNA regulation, ROS production and aging.
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Affiliation(s)
- Nicolas Pichaud
- Laboratory of Comparative Biochemistry and Physiology, Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Roxanne Bérubé
- Laboratoire de Physiologie Animale Intégrative, Département de Biologie, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - Geneviève Côté
- Laboratoire de Physiologie Animale Intégrative, Département de Biologie, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - Claude Belzile
- Institut des Sciences de la mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - France Dufresne
- Laboratoire d'Écologie Moléculaire, Département de Biologie, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - Geneviève Morrow
- Laboratoire de Génétique Cellulaire et Développementale, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Quebec City, QC, Canada
| | - Robert M Tanguay
- Laboratoire de Génétique Cellulaire et Développementale, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Quebec City, QC, Canada
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Pierre U Blier
- Laboratoire de Physiologie Animale Intégrative, Département de Biologie, Université du Québec à Rimouski, Rimouski, QC, Canada
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15
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Unraveling the intricate biodiversity of the benthic harpacticoid genus Nannopus (Copepoda, Harpacticoida, Nannopodidae) in Korean waters. Mol Phylogenet Evol 2019; 130:366-379. [DOI: 10.1016/j.ympev.2018.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/17/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022]
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16
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Graham AM, Barreto FS. Novel microRNAs are associated with population divergence in transcriptional response to thermal stress in an intertidal copepod. Mol Ecol 2018; 28:584-599. [PMID: 30548575 DOI: 10.1111/mec.14973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/29/2022]
Abstract
The role of gene expression in adaptation to differing thermal environments has been assayed extensively. Yet, in most natural systems, analyses of gene expression reveal only one level of the complexity of regulatory machineries. MicroRNAs (miRNAs) are small noncoding RNAs which are key components of many gene regulatory networks, and they play important roles in a variety of cellular pathways by modulating post-transcriptional quantities of mRNA available for protein synthesis. The characterization of miRNA loci and their regulatory dynamics in nonmodel systems are still largely understudied. In this study, we examine the role of miRNAs in response to high thermal stress in the intertidal copepod Tigriopus californicus. Allopatric populations of this species show varying levels of local adaptation with respect to thermal regimes, and previous studies showed divergence in gene expression between populations from very different thermal environments. We examined the transcriptional response to temperature stress in two populations separated by only 8 km by utilizing RNA-seq to quantify both mRNA and miRNA levels. Using the currently available genome sequence, we first describe the repertoire of miRNAs in T. californicus and assess the degree to which transcriptional response to temperature stress is governed by miRNA activity. The two populations showed large differences in the number of genes involved, the magnitude of change in commonly used genes and in the number of miRNAs involved in transcriptional modulation during stress. Our results suggest that an increased level of regulatory network complexity may underlie improved survivorship under thermal stress in one of the populations.
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Affiliation(s)
- Allie M Graham
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon
| | - Felipe S Barreto
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon
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Barreto FS, Watson ET, Lima TG, Willett CS, Edmands S, Li W, Burton RS. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Nat Ecol Evol 2018; 2:1250-1257. [DOI: 10.1038/s41559-018-0588-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
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18
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19
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Weydmann A, Przyłucka A, Lubośny M, Walczyńska KS, Serrão EA, Pearson GA, Burzyński A. Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non-coding regions. Sci Rep 2017; 7:13702. [PMID: 29057900 PMCID: PMC5651803 DOI: 10.1038/s41598-017-13807-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
We determined the nearly complete mitochondrial genomes of the Arctic Calanus glacialis and its North Atlantic sibling Calanus finmarchicus, which are key zooplankton components in marine ecosystems. The sequenced part of C. glacialis mitogenome is 27,342 bp long and consists of two contigs, while for C. finmarchicus it is 29,462 bp and six contigs, what makes them the longest reported copepod mitogenomes. The typical set of metazoan mitochondrial genes is present in these mitogenomes, although the non-coding regions (NCRs) are unusually long and complex. The mitogenomes of the closest species C. glacialis and C. finmarchicus, followed by the North Pacific C. sinicus, are structurally similar and differ from the much more typical of deep-water, Arctic C. hyperboreus. This evolutionary trend for the expansion of NCRs within the Calanus mitogenomes increases mitochondrial DNA density, what resulted in its similar density to the nuclear genome. Given large differences in the length and structure of C. glacialis and C. finmarchicus mitogenomes, we conclude that the species are genetically distinct and thus cannot hybridize. The molecular resources presented here: the mitogenomic and rDNA sequences, and the database of repetitive elements should facilitate the development of genetic markers suitable in pursuing evolutionary research in copepods.
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Affiliation(s)
- Agata Weydmann
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland.
- University of Gdansk, Institute of Oceanography, Gdynia, 81-378, Poland.
| | | | - Marek Lubośny
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
| | | | - Ester A Serrão
- University of Algarve, CCMAR, CIMAR, Faro, 8005-139, Portugal
| | | | - Artur Burzyński
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
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20
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Fazhan H, Waiho K, Shahreza MS. A simple and efficient total genomic DNA extraction method for individual zooplankton. SPRINGERPLUS 2016; 5:2049. [PMID: 27995026 PMCID: PMC5130931 DOI: 10.1186/s40064-016-3724-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/21/2016] [Indexed: 01/08/2023]
Abstract
Molecular approaches are widely applied in species identification and taxonomic studies of minute zooplankton. One of the most focused zooplankton nowadays is from Subclass Copepoda. Accurate species identification of all life stages of the generally small sized copepods through molecular analysis is important, especially in taxonomic and systematic assessment of harpacticoid copepod populations and to understand their dynamics within the marine community. However, total genomic DNA (TGDNA) extraction from individual harpacticoid copepods can be problematic due to their small size and epibenthic behavior. In this research, six TGDNA extraction methods done on individual harpacticoid copepods were compared. The first new simple, feasible, efficient and consistent TGDNA extraction method was designed and compared with the commercial kit and modified available TGDNA extraction methods. The newly described TGDNA extraction method, "Incubation in PCR buffer" method, yielded good and consistent results based on the high success rate of PCR amplification (82%) compared to other methods. Coupled with its relatively consistent and economical method the "Incubation in PCR buffer" method is highly recommended in the TGDNA extraction of other minute zooplankton species.
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Affiliation(s)
- Hanafiah Fazhan
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu (UMT), 21030 Kuala Terengganu, Terengganu Malaysia
| | - Khor Waiho
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu (UMT), 21030 Kuala Terengganu, Terengganu Malaysia
| | - Md. Sheriff Shahreza
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu (UMT), 21030 Kuala Terengganu, Terengganu Malaysia
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21
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Easton EE, Thistle D. Do some deep‐sea, sediment‐dwelling species of harpacticoid copepods have 1000‐km‐scale range sizes? Mol Ecol 2016; 25:4301-18. [DOI: 10.1111/mec.13744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- E. E. Easton
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
| | - D. Thistle
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
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DNA Barcoding of Metazoan Zooplankton Copepods from South Korea. PLoS One 2016; 11:e0157307. [PMID: 27383475 PMCID: PMC4934703 DOI: 10.1371/journal.pone.0157307] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 05/30/2016] [Indexed: 12/03/2022] Open
Abstract
Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis–Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae–Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica–Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica–Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.
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Pereira RJ, Barreto FS, Pierce NT, Carneiro M, Burton RS. Transcriptome-wide patterns of divergence during allopatric evolution. Mol Ecol 2016; 25:1478-93. [DOI: 10.1111/mec.13579] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/03/2015] [Accepted: 01/06/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Ricardo J. Pereira
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Felipe S. Barreto
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331 USA
| | - N. Tessa Pierce
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
| | - Miguel Carneiro
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Ronald S. Burton
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
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Shen X, Tsang LM, Chu KH, Achituv Y, Chan BKK. Mitochondrial genome of the intertidal acorn barnacle Tetraclita serrata Darwin, 1854 (Crustacea: Sessilia): Gene order comparison and phylogenetic consideration within Sessilia. Mar Genomics 2015; 22:63-9. [PMID: 25907711 DOI: 10.1016/j.margen.2015.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 04/09/2015] [Accepted: 04/09/2015] [Indexed: 01/11/2023]
Abstract
The complete mitochondrial genome of the intertidal barnacle Tetraclita serrata Darwin, 1854 (Crustacea: Maxillopoda: Sessilia) is presented. The genome is a circular molecule of 15,200 bp, which encodes 13 PCGs, 2 ribosomal RNA genes, and 22 transfer RNA genes. All non-coding regions are 591 bp in length, with the longest one speculated as the control region (389 bp), which is located between srRNA and trnK. The overall A+T content of the mitochondrial genome of T. serrata is 65.4%, which is lowest among all the eight mitochondrial genomes reported from sessile barnacles. There are variations of initiation and stop codons in the reported sessile barnacle mitochondrial genomes. Large-scale gene rearrangements are found in these genomes as compared to the pancrustacean ground pattern. ML and Bayesian analyses of all 15 complete mitochondrial genomes available from Maxillopoda lead to identical phylogenies. The phylogenetic tree based on mitochondrial PCGs shows that Argulus americanus (Branchiura) cluster with Armillifer armillatus (Pentastomida), distinct from all ten species from Cirripedia. Within the order Sessilia, Amphibalanus amphitrite (Balanidae) clusters with Striatobalanus amaryllis (Archaeobalanidae), and Nobia grandis (Pyrgomatidae). However, the two Megabalanus (Balanidae) are separated from the above grouping, resulting in non-monophyly of the family Balanidae. Moreover, the two Megabalanus have large-scale rearrangements as compared to the gene order shared by former three species. Therefore, both phylogenetic analysis using PCG sequences and gene order comparison suggest that Balanidae is not a monophyletic group. Given the limited taxa and moderate support values of the internal branches, the non-monophyly of the family Balanidae requires further verification.
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Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science/Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China; Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ling Ming Tsang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Yair Achituv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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25
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Saunier A, Garcia P, Becquet V, Marsaud N, Escudié F, Pante E. Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities. BMC Evol Biol 2014; 14:259. [PMID: 25527898 PMCID: PMC4302422 DOI: 10.1186/s12862-014-0259-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Allopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous F ST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform. RESULTS The mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNA (Met) and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations. CONCLUSIONS Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.
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Affiliation(s)
- Alice Saunier
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Pascale Garcia
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Vanessa Becquet
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Nathalie Marsaud
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Frédéric Escudié
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Eric Pante
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
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26
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Zagoskin MV, Lazareva VI, Grishanin AK, Mukha DV. Phylogenetic information content of Copepoda ribosomal DNA repeat units: ITS1 and ITS2 impact. BIOMED RESEARCH INTERNATIONAL 2014; 2014:926342. [PMID: 25215300 PMCID: PMC4151598 DOI: 10.1155/2014/926342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/08/2014] [Accepted: 07/08/2014] [Indexed: 11/17/2022]
Abstract
The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.
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Affiliation(s)
- Maxim V. Zagoskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Street. 3, Moscow 119991, Russia
| | - Valentina I. Lazareva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Andrey K. Grishanin
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
- Dubna International University for Nature, Society and Man, Universitetskaya Street 19, Dubna 141980, Russia
| | - Dmitry V. Mukha
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Street. 3, Moscow 119991, Russia
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27
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Christie AE. Prediction of the peptidomes of Tigriopus californicus and Lepeophtheirus salmonis (Copepoda, Crustacea). Gen Comp Endocrinol 2014; 201:87-106. [PMID: 24613138 DOI: 10.1016/j.ygcen.2014.02.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/03/2014] [Accepted: 02/12/2014] [Indexed: 11/23/2022]
Abstract
Transcriptome mining is a powerful method for crustacean peptide discovery, especially when large sequence datasets are available and an appropriate reference is extant. Recently, a 206,041-sequence transcriptome for the copepod Calanus finmarchicus was mined for peptide-encoding transcripts, with ones for 17 families/subfamilies identified. Here, the deduced Calanus pre/preprohormones were used as templates for peptide discovery in the copepods Tigriopus californicus and Lepeophtheirus salmonis; large transcriptome shotgun assembly datasets are publicly accessible for both species. Sixty-five Tigriopus and 17 Lepeophtheirus transcripts, encompassing 22 and 13 distinct peptide families/subfamilies, respectively, were identified, with the structures of 161 and 70 unique mature peptides predicted from the deduced precursors. The identified peptides included members of the allatostatin A, allatostatin C, bursicon α, bursicon β, CAPA/periviscerokinin/pyrokinin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, FLRFamide, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, and tachykinin-related peptide families, most of which possess novel structures, though isoforms from other copepods are known. Of particular note was the discovery of novel isoforms of adipokinetic hormone-corazonin-like peptide, allatotropin, corazonin, eclosion hormone and intocin, peptide families previously unidentified in copepods. In addition, Tigriopus precursors for two previously unknown peptide groups were discovered, one encoding GSEFLamides and the other DXXRLamides; precursors for the novel FXGGXamide family were identified from both Tigriopus and Lepeophtheirus. These data not only greatly expand the catalog of known copepod peptides, but also provide strong foundations for future functional studies of peptidergic signaling in members of this ecologically important crustacean subclass.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
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Easton EE, Darrow EM, Spears T, Thistle D. The mitochondrial genomes of Amphiascoides atopus and Schizopera knabeni (Harpacticoida: Miraciidae) reveal similarities between the copepod orders Harpacticoida and Poecilostomatoida. Gene 2014; 538:123-37. [DOI: 10.1016/j.gene.2013.12.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/24/2013] [Indexed: 12/15/2022]
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29
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Burton RS, Pereira RJ, Barreto FS. Cytonuclear Genomic Interactions and Hybrid Breakdown. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135758] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
| | - Ricardo J. Pereira
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
| | - Felipe S. Barreto
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202; , ,
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30
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Albertin W, da Silva T, Rigoulet M, Salin B, Masneuf-Pomarede I, de Vienne D, Sicard D, Bely M, Marullo P. The mitochondrial genome impacts respiration but not fermentation in interspecific Saccharomyces hybrids. PLoS One 2013; 8:e75121. [PMID: 24086452 PMCID: PMC3781082 DOI: 10.1371/journal.pone.0075121] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/08/2013] [Indexed: 01/30/2023] Open
Abstract
In eukaryotes, mitochondrial DNA (mtDNA) has high rate of nucleotide substitution leading to different mitochondrial haplotypes called mitotypes. However, the impact of mitochondrial genetic variant on phenotypic variation has been poorly considered in microorganisms because mtDNA encodes very few genes compared to nuclear DNA, and also because mitochondrial inheritance is not uniparental. Here we propose original material to unravel mitotype impact on phenotype: we produced interspecific hybrids between S. cerevisiae and S. uvarum species, using fully homozygous diploid parental strains. For two different interspecific crosses involving different parental strains, we recovered 10 independent hybrids per cross, and allowed mtDNA fixation after around 80 generations. We developed PCR-based markers for the rapid discrimination of S. cerevisiae and S. uvarum mitochondrial DNA. For both crosses, we were able to isolate fully isogenic hybrids at the nuclear level, yet possessing either S. cerevisiae mtDNA (Sc-mtDNA) or S. uvarum mtDNA (Su-mtDNA). Under fermentative conditions, the mitotype has no phenotypic impact on fermentation kinetics and products, which was expected since mtDNA are not necessary for fermentative metabolism. Alternatively, under respiratory conditions, hybrids with Sc-mtDNA have higher population growth performance, associated with higher respiratory rate. Indeed, far from the hypothesis that mtDNA variation is neutral, our work shows that mitochondrial polymorphism can have a strong impact on fitness components and hence on the evolutionary fate of the yeast populations. We hypothesize that under fermentative conditions, hybrids may fix stochastically one or the other mt-DNA, while respiratory environments may increase the probability to fix Sc-mtDNA.
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Affiliation(s)
- Warren Albertin
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche CEnologie, Villenave d’Ornon, France
- Bordeaux Sciences Agro, Gradignan, France
| | - Telma da Silva
- INRA, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Michel Rigoulet
- CNRS, UMR 5095, Institute of Biochemistry and Genetics of the Cell, Bordeaux, France
- Univ. de Bordeaux, IBGC, UMR 5095, Bordeaux, France
| | - Benedicte Salin
- CNRS, UMR 5095, Institute of Biochemistry and Genetics of the Cell, Bordeaux, France
- Univ. de Bordeaux, IBGC, UMR 5095, Bordeaux, France
| | - Isabelle Masneuf-Pomarede
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche CEnologie, Villenave d’Ornon, France
- Bordeaux Sciences Agro, Gradignan, France
| | - Dominique de Vienne
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Marina Bely
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche CEnologie, Villenave d’Ornon, France
| | - Philippe Marullo
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche CEnologie, Villenave d’Ornon, France
- BIOLAFFORT, Bordeaux, France
- * E-mail:
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Barreto FS, Burton RS. Elevated oxidative damage is correlated with reduced fitness in interpopulation hybrids of a marine copepod. Proc Biol Sci 2013; 280:20131521. [PMID: 23902912 DOI: 10.1098/rspb.2013.1521] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aerobic energy production occurs via the oxidative phosphorylation pathway (OXPHOS), which is critically dependent on interactions between the 13 mitochondrial DNA (mtDNA)-encoded and approximately 70 nuclear-encoded protein subunits. Disruptive mutations in any component of OXPHOS can result in impaired ATP production and exacerbated oxidative stress; in mammalian systems, such mutations are associated with ageing as well as numerous diseases. Recent studies have suggested that oxidative stress plays a role in fitness trade-offs in life-history evolution and functional ecology. Here, we show that outcrossing between populations with divergent mtDNA can exacerbate cellular oxidative stress in hybrid offspring. In the copepod Tigriopus californicus, we found that hybrids that showed evidence of fitness breakdown (low fecundity) also exhibited elevated levels of oxidative damage to DNA, whereas those with no clear breakdown did not show significantly elevated damage. The extent of oxidative stress in hybrids appears to be dependent on the degree of genetic divergence between their respective parental populations, but this pattern requires further testing using multiple crosses at different levels of divergence. Given previous evidence in T. californicus that hybridization disrupts nuclear/mitochondrial interactions and reduces hybrid fitness, our results suggest that such negative intergenomic epistasis may also increase the production of damaging cellular oxidants; consequently, mtDNA evolution may play a significant role in generating postzygotic isolating barriers among diverging populations.
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Affiliation(s)
- Felipe S Barreto
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA.
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Kim S, Lim BJ, Min GS, Choi HG. The complete mitochondrial genome of Arctic Calanus hyperboreus (Copepoda, Calanoida) reveals characteristic patterns in calanoid mitochondrial genome. Gene 2013; 520:64-72. [DOI: 10.1016/j.gene.2012.09.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/10/2012] [Accepted: 09/20/2012] [Indexed: 12/13/2022]
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Pritchard VL, Knutson VL, Lee M, Zieba J, Edmands S. Fitness and morphological outcomes of many generations of hybridization in the copepod Tigriopus californicus. J Evol Biol 2012; 26:416-33. [DOI: 10.1111/jeb.12060] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 12/27/2022]
Affiliation(s)
- V. L. Pritchard
- Department of Biological Sciences; University of Southern California; Los Angeles CA USA
| | - V. L. Knutson
- Department of Biological Sciences; University of Southern California; Los Angeles CA USA
| | - M. Lee
- Department of Biological Sciences; University of Southern California; Los Angeles CA USA
| | - J. Zieba
- Department of Biological Sciences; University of Southern California; Los Angeles CA USA
| | - S. Edmands
- Department of Biological Sciences; University of Southern California; Los Angeles CA USA
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Pritchard VL, Edmands S. THE GENOMIC TRAJECTORY OF HYBRID SWARMS: OUTCOMES OF REPEATED CROSSES BETWEEN POPULATIONS OFTIGRIOPUS CALIFORNICUS. Evolution 2012; 67:774-91. [DOI: 10.1111/j.1558-5646.2012.01814.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Burton RS, Barreto FS. A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities? Mol Ecol 2012; 21:4942-57. [PMID: 22994153 DOI: 10.1111/mec.12006] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/18/2012] [Accepted: 07/25/2012] [Indexed: 01/07/2023]
Abstract
Evolution in allopatric populations can lead to incompatibilities that result in reduced hybrid fitness and ultimately reproductive isolation upon secondary contact. The Dobzhansky-Muller (DM) model nicely accounts for the evolution of such incompatibilities. Although DM incompatibilities were originally conceived as resulting of interactions between nuclear genes, recent studies have documented cases where incompatibilities have arisen between nuclear and mitochondrial genomes (mtDNA). Although mtDNA comprises only a tiny component (typically <<0.01%) of an organism's genetic material, several features of mtDNA may lead to a disproportionate contribution to the evolution of hybrid incompatibilities: (i) essentially all functions of mtDNA require interaction with nuclear gene products. All mtDNA-encoded proteins are components of the oxidative phosphorylation (OXPHOS) system and all mtDNA-encoded RNAs are part of the mitochondrial protein synthetic machinery; both processes require interaction with nuclear-encoded proteins for function. (ii) Transcription and replication of mtDNA also involve mitonuclear interactions as nuclear-encoded proteins must bind to regulatory motifs in the mtDNA to initiate these processes. (iii) Although features of mtDNA vary amongst taxa, metazoan mtDNA is typically characterized by high nucleotide substitution rates, lack of recombination and reduced effective population sizes that collectively lead to increased chance fixation of mildly deleterious mutations. Combined, these features create an evolutionary dynamic where rapid mtDNA evolution favours compensatory nuclear gene evolution, ultimately leading to co-adaptation of mitochondrial and nuclear genomes. When previously isolated lineages hybridize in nature or in the lab, intergenomic co-adaptation is disrupted and hybrid breakdown is observed; the role of intergenomic co-adaptation in hybrid breakdown and speciation will generally be most pronounced when rates of mtDNA evolution are high or when restricted gene flow results in significant population differentiation.
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Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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Hicks KA, Howe DK, Leung A, Denver DR, Estes S. In vivo quantification reveals extensive natural variation in mitochondrial form and function in Caenorhabditis briggsae. PLoS One 2012; 7:e43837. [PMID: 22952781 PMCID: PMC3429487 DOI: 10.1371/journal.pone.0043837] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 07/30/2012] [Indexed: 12/18/2022] Open
Abstract
We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.
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Affiliation(s)
- Kiley A. Hicks
- Biology Department, Portland State University, Portland, Oregon, United States of America
| | - Dana K. Howe
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Aubrey Leung
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Dee R. Denver
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Suzanne Estes
- Biology Department, Portland State University, Portland, Oregon, United States of America
- * E-mail:
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Quantifying the Elevation of Mitochondrial DNA Evolutionary Substitution Rates Over Nuclear Rates in the Intertidal Copepod Tigriopus californicus. J Mol Evol 2012; 74:310-8. [DOI: 10.1007/s00239-012-9508-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
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Pichaud N, Ballard JWO, Tanguay RM, Blier PU. Naturally occurring mitochondrial DNA haplotypes exhibit metabolic differences: insight into functional properties of mitochondria. Evolution 2012; 66:3189-97. [PMID: 23025608 DOI: 10.1111/j.1558-5646.2012.01683.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Linking the mitochondrial genotype and the organismal phenotype is of paramount importance in evolution of mitochondria. In this study, we determined the differences in catalytic properties of mitochondria dictated by divergences in the siII and siIII haplogroups of Drosophila simulans using introgressions of siII mtDNA type into the siIII nuclear background. We used a novel in situ method (permeabilized fibers) that allowed us to accurately measure the consumption of oxygen by mitochondria in constructed siII-introgressed flies and in siIII-control flies. Our results showed that the catalytic capacity of the electron transport system is not impaired by introgressions, suggesting that the functional properties of mitochondria are tightly related to the mtDNA haplogroup and not to the nuclear DNA or to the mito-nuclear interactions. This is the first study, to our knowledge, that demonstrates a naturally occurring haplogroup can confer specific functional differences in aspects of mitochondrial metabolism. This study illustrates the importance of mtDNA changes on organelle evolution and highlights the potential bioenergetic and metabolic impacts that divergent mitochondrial haplogroups may have upon a wide variety of species including humans.
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Affiliation(s)
- Nicolas Pichaud
- Laboratoire de biologie intégrative, Département de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Québec, Canada G5L 3A1.
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Yasuike M, Leong J, Jantzen SG, von Schalburg KR, Nilsen F, Jones SRM, Koop BF. Genomic resources for sea lice: analysis of ESTs and mitochondrial genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:155-166. [PMID: 21748342 PMCID: PMC3280385 DOI: 10.1007/s10126-011-9398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 06/22/2011] [Indexed: 05/31/2023]
Abstract
Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an important economic market in North America, South America, and Northern Europe. Infections with sea lice can result in significant production losses. A compilation of genomic information on different genera of sea lice is an important resource for understanding their biology as well as for the study of population genetics and control strategies. We report on over 150,000 expressed sequence tags (ESTs) from five different species (Pacific Lepeophtheirus salmonis (49,672 new ESTs in addition to 14,994 previously reported ESTs), Atlantic L. salmonis (57,349 ESTs), Caligus clemensi (14,821 ESTs), Caligus rogercresseyi (32,135 ESTs), and Lernaeocera branchialis (16,441 ESTs)). For each species, ESTs were assembled into complete or partial genes and annotated by comparisons to known proteins in public databases. In addition, whole mitochondrial (mt) genome sequences of C. clemensi (13,440 bp) and C. rogercresseyi (13,468 bp) were determined and compared to L. salmonis. Both nuclear and mtDNA genes show very high levels of sequence divergence between these ectoparastic copepods suggesting that the different species of sea lice have been in existence for 37-113 million years and that parasitic association with salmonids is also quite ancient. Our ESTs and mtDNA data provide a novel resource for the study of sea louse biology, population genetics, and control strategies. This genomic information provides the material basis for the development of a 38K sea louse microarray that can be used in conjunction with our existing 44K salmon microarray to study host-parasite interactions at the molecular level. This report represents the largest genomic resource for any copepod species to date.
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Affiliation(s)
- Motoshige Yasuike
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
- Present Address: Aquatic Genomics Research Center, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Jong Leong
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
| | - Stuart G. Jantzen
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
| | | | - Frank Nilsen
- Department of Biology, University of Bergen, 5020 Bergen, Norway
| | - Simon R. M. Jones
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7 Canada
| | - Ben F. Koop
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
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40
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Bron JE, Frisch D, Goetze E, Johnson SC, Lee CE, Wyngaard GA. Observing copepods through a genomic lens. Front Zool 2011; 8:22. [PMID: 21933388 PMCID: PMC3184258 DOI: 10.1186/1742-9994-8-22] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 09/20/2011] [Indexed: 01/08/2023] Open
Abstract
Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to provide genomics tools for copepods. Summary Genomics research on copepods is needed to extend our exploration and characterization of their fundamental biological traits, so that we can better understand how copepods function and interact in diverse environments. Availability of large scale genomics resources will also open doors to a wide range of systems biology type studies that view the organism as the fundamental system in which to address key questions in ecology and evolution.
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Affiliation(s)
- James E Bron
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, Scotland, UK.
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41
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Kartavtsev YP. Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics. Mar Genomics 2011; 4:71-81. [DOI: 10.1016/j.margen.2011.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 01/26/2011] [Accepted: 02/23/2011] [Indexed: 11/15/2022]
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Klimov PB, Knowles LL. Repeated parallel evolution of minimal rRNAs revealed from detailed comparative analysis. ACTA ACUST UNITED AC 2011; 102:283-93. [PMID: 21422103 DOI: 10.1093/jhered/esr005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The concept of a minimal ribosomal RNA-containing ribosome, a structure with a minimal set of elements capable of providing protein biosynthesis, is essential for understanding this fundamental cellular process. Nematodes and trypanosomes have minimal mitochondrial rRNAs and detailed reconstructions of their secondary structures indicate that certain conserved helices have been lost in these taxa. In contrast, several recent studies on acariform mites have argued that minimal rRNAs may evolve via shortening of secondary structure elements but not the loss of these elements as shown for trypanosomes and nematodes. Based on extensive structural analysis of chelicerate arthropods, we demonstrate that extremely short rRNAs of acariform mites share certain structural modifications with nematodes and trypanosomes: loss of helices of the GTPase region and divergence in the evolutionarily conserved connecting loop between helices H1648 and H1764 of the large subunit rRNA. These highly concerted parallel modifications indicate that minimal rRNAs were generated under the strong selection that favored or tolerated reductions of helices in particular locations while maintaining the functionality of the rRNA molecules throughout evolution. We also discuss potential evolution of minimal rRNAs and atypical transfer RNAs.
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Affiliation(s)
- Pavel B Klimov
- University of Michigan, Museum of Zoology, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA.
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43
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Minxiao W, Song S, Chaolun L, Xin S. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies. BMC Genomics 2011; 12:73. [PMID: 21269523 PMCID: PMC3041745 DOI: 10.1186/1471-2164-12-73] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 01/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of C. sinicus mitogenomes provide a solid foundation for population genetic studies.
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Affiliation(s)
- Wang Minxiao
- KLMEES and JBMERS, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
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44
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Barreto FS, Moy GW, Burton RS. Interpopulation patterns of divergence and selection across the transcriptome of the copepod Tigriopus californicus. Mol Ecol 2010; 20:560-72. [PMID: 21199025 DOI: 10.1111/j.1365-294x.2010.04963.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The accumulation of genetic incompatibilities between isolated populations is thought to lead to the evolution of intrinsic postzygotic isolation. The molecular basis for these mechanisms, however, remains poorly understood. The intertidal copepod Tigriopus californicus provides unique opportunities for addressing mechanistic questions regarding the early stages of speciation; hybrids between highly divergent populations are fertile and viable, but exhibit reduced fitness at the F(2) or later generations. Given the current scarcity of genomic information in taxa at incipient stages of reproductive isolation, we utilize high-throughout 454 pyrosequencing to characterize a substantial fraction of protein-coding regions (the transcriptome) of T. californicus. Our sequencing effort was divided equally between two divergent populations in order to estimate levels of divergence and to reveal patterns of selection across the transcriptome. Assembly of sequences generated over 40,000 putatively unique transcripts (unigenes) for each population, 19,622 of which were orthologous between populations. BLAST searches of public databases determined protein identity and functional features for 15,402 and 12,670 unigenes, respectively. Based on rates of nonsynonymous and synonymous substitutions in 5897 interpopulation orthologs (those >150 bp and with at least 2X coverage), we identified 229 potential targets of positive selection. Many of these genes are predicted to be involved in several metabolic processes, and to function in hydrolase, peptidase and binding activities. The library of T. californicus coding regions, annotated with their predicted functions and level of divergence, will serve as an invaluable resource for elucidating molecular mechanisms underlying the early stages of speciation.
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Affiliation(s)
- Felipe S Barreto
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA 92037, USA.
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45
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Arnqvist G, Dowling DK, Eady P, Gay L, Tregenza T, Tuda M, Hosken DJ. Genetic architecture of metabolic rate: environment specific epistasis between mitochondrial and nuclear genes in an insect. Evolution 2010; 64:3354-63. [PMID: 20874734 DOI: 10.1111/j.1558-5646.2010.01135.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extent to which mitochondrial DNA (mtDNA) variation is involved in adaptive evolutionary change is currently being reevaluated. In particular, emerging evidence suggests that mtDNA genes coevolve with the nuclear genes with which they interact to form the energy producing enzyme complexes in the mitochondria. This suggests that intergenomic epistasis between mitochondrial and nuclear genes may affect whole-organism metabolic phenotypes. Here, we use crossed combinations of mitochondrial and nuclear lineages of the seed beetle Callosobruchus maculatus and assay metabolic rate under two different temperature regimes. Metabolic rate was affected by an interaction between the mitochondrial and nuclear lineages and the temperature regime. Sequence data suggests that mitochondrial genetic variation has a role in determining the outcome of this interaction. Our genetic dissection of metabolic rate reveals a high level of complexity, encompassing genetic interactions over two genomes, and genotype × genotype × environment interactions. The evolutionary implications of these results are twofold. First, because metabolic rate is at the root of life histories, our results provide insights into the complexity of life-history evolution in general, and thermal adaptation in particular. Second, our results suggest a mechanism that could contribute to the maintenance of nonneutral mtDNA polymorphism.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Evolution, University of Uppsala, SE-752 36 Uppsala, Sweden.
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Ki JS, Hop H, Kim SJ, Kim IC, Park HG, Lee JS. Complete mitochondrial genome sequence of the Arctic gammarid, Onisimus nanseni (Crustacea; Amphipoda): Novel gene structures and unusual control region features. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:105-15. [DOI: 10.1016/j.cbd.2010.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 02/04/2010] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
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Phylogeny of the freshwater copepod Mesocyclops (Crustacea: Cyclopidae) based on combined molecular and morphological data, with notes on biogeography. Mol Phylogenet Evol 2010; 55:753-64. [DOI: 10.1016/j.ympev.2010.02.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 02/24/2010] [Accepted: 02/25/2010] [Indexed: 11/18/2022]
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Edmands S, Northrup SL, Hwang AS. MALADAPTED GENE COMPLEXES WITHIN POPULATIONS OF THE INTERTIDAL COPEPODTIGRIOPUS CALIFORNICUS? Evolution 2009; 63:2184-92. [DOI: 10.1111/j.1558-5646.2009.00689.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Ki JS, Park HG, Lee JS. The complete mitochondrial genome of the cyclopoid copepod Paracyclopina nana: a highly divergent genome with novel gene order and atypical gene numbers. Gene 2009; 435:13-22. [PMID: 19393182 DOI: 10.1016/j.gene.2009.01.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 12/22/2008] [Accepted: 01/07/2009] [Indexed: 11/29/2022]
Abstract
In this paper, we describe the complete mitogenome of the cyclopoid copepod Paracyclopina nana with emphasis on the highly rearranged gene order and high divergence against published copepod mitogenomes. The P. nana mtDNA is 15,981 bp in length (70.9% AT) and consists of 37 genes (12 protein-coding genes, 2 rRNAs, 23 tRNAs) that are atypical for metazoan mitogenomes. Unusually, it contains an extra tRNA (tRNA-Ala) but it does not contain the ATPase 8 gene. The P. nana mitogenome has a long putative control region with high AT content (1351 bp, 77.0% AT). The Cyt b was considerably short in length, compared to other crustaceans. Compared to typical mitogenomes of arthropods and copepods, the gene order of the P. nana mitogenome is highly rearranged with a novel gene structure. In addition, P. nana has highly divergent mt genes (mostly less than 50%), judged by amino acid substitution. We present the first complete mitogenome sequence from a cyclopoid copepod, thereby increasing our understanding of copepod and crustacean evolution from the mitochondrial point of view.
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Affiliation(s)
- Jang-Seu Ki
- Department of Chemistry, Hanyang University, Seoul, South Korea
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THUM RYANA, HARRISON RICHARDG. Deep genetic divergences among morphologically similar and parapatric Skistodiaptomus (Copepoda: Calanoida: Diaptomidae) challenge the hypothesis of Pleistocene speciation. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01105.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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