The tyrosyl-DNA phosphodiesterase gene family in Medicago truncatula Gaertn.: bioinformatic investigation and expression profiles in response to copper- and PEG-mediated stress

The Tdp1 gene encoding tyrosyl-DNA phosphodiesterase has been extensively investigated in animal cells, due to the role of this enzyme in the repair of topoisomerase I-DNA covalent lesions. In contrast, information in this regard is totally missing in plants. We report for the first time in plants on the Tdp1 gene family from barrel medic (Medicago truncatula Gaertn.), composed of two members, hereby named MtTdp1α and MtTdp1β. The expression profiles of MtTdp1α and MtTdp1β genes were evaluated in plantlets grown in vitro using copper and polyethylene glycol (PEG 6000) as stress agents. In situ detection of reactive oxygen species (ROS) was carried out by histochemical staining, while the level of oxidative DNA damage, quantified in terms of 7,8-dihydro-8-oxoguanine (8-oxo-dG), increased up to 7.4- and 6.7-fold in response to copper and PEG 6000 treatments, respectively. Quantitative real-time polymerase chain reaction revealed that both Tdp1 genes were significantly up-regulated in response to copper and PEG. The Tdp1 genes were also significantly up-regulated during seed rehydration, an aspect of seed physiology in which DNA repair is a key component. Thus, the Tdp1 genes might be used as novel tools for improving stress tolerance in crops. The expression patterns of the barrel medic top1α and top1β genes, encoding distinct isoforms of DNA topoisomerase I, were also analyzed and discussed to acquire additional information on their specific functions, closely related to that of the Tdp1 gene in animal cells.     

Seed germination at different temperatures and water stress levels,and seedling emergence from different depths of Ziziphus lotus

Ziziphus lotus (L.) Lam. is a deciduous shrub with intricately branched stems in the Rhamnaceae family. It's a dominant and economically important species widely distributed in active sand dunes in the southern desert of Tunisia. To provide basic information for its conservation and reintroduction, we studied the influence of environmental factors on seed germination patterns. The germination responses of seeds were determined over a wide range of constant temperatures (10–50 °C), polyethylene glycol (PEG)-6000 solutions of different osmotic potentials (0 to − 1 MPa) and burial depths (1–10 cm). Temperatures between 15 and 45 °C seem to be favorable for the germination of this species. Germination was inhibited by either an increase or decrease in temperature from the most suitable temperature found (35 °C). The highest germination percentages (100%) were obtained under control conditions without PEG, and increasing moisture stress progressively inhibited seed germination, which was less than 5% at − 1 MPa. When tested for germination in distilled water, after PEG treatments, seeds germinated to the same extent as when fresh. When seeds buried deeply, there was a significant decrease in seedling emergence percentage and rate. Seedlings of Z. lotus emerged well at depths of 1–2 cm and could not emerge when sand burial depth was > 4 cm.     

Prior hydration of Brassica tournefortii seeds reduces the stimulatory effect of karrikinolide on germination and increases seed sensitivity to abscisic acid

Background and Aims

The smoke-derived compound karrikinolide (KAR₁) shows significant potential as a trigger for the synchronous germination of seeds in a variety of plant-management contexts, from weed seeds in paddocks, to native seeds when restoring degraded lands. Understanding how KAR₁ interacts with seed physiology is a necessary precursor to the development of the compound as an efficient and effective management tool. This study tested the ability of KAR₁ to stimulate germination of seeds of the global agronomic weed Brassica tournefortii, at different hydration states, to gain insight into how the timing of KAR₁ applications in the field should be managed relative to rain events.

Methods

Seeds of B. tournefortii were brought to five different hydration states [equilibrated at 15 % relative humidity (RH), 47 % RH, 96 % RH, fully imbibed, or re-dried to 15 % RH following maximum imbibition] then exposed to 1 nm or 1 µm KAR₁ for one of five durations (3 min, 1 h, 24 h, 14 d or no exposure).

Key Results

Dry seeds with no history of imbibition were the most sensitive to KAR₁; sensitivity was lower in seeds that were fully imbibed or fully imbibed then re-dried. In addition, reduced sensitivity to KAR₁ was associated with an increased sensitivity to exogenously applied abscisic acid (ABA).

Conclusions

Seed water content and history of imbibition were found to significantly influence whether seeds germinate in response to KAR₁. To optimize the germination response of seeds, KAR₁ should be applied to dry seeds, when sensitivity to ABA is minimized.     

Lesion-Induced Mutation in the Hyperthermophilic Archaeon Sulfolobus acidocaldarius and Its Avoidance by the Y-Family DNA Polymerase Dbh

Hyperthermophilic archaea offer certain advantages as models of genome replication, and Sulfolobus Y-family polymerases Dpo4 (S. solfataricus) and Dbh (S. acidocaldarius) have been studied intensively in vitro as biochemical and structural models of trans-lesion DNA synthesis (TLS). However, the genetic functions of these enzymes have not been determined in the native context of living cells. We developed the first quantitative genetic assays of replication past defined DNA lesions and error-prone motifs in Sulfolobus chromosomes and used them to measure the efficiency and accuracy of bypass in normal and dbh⁻ strains of Sulfolobus acidocaldarius. Oligonucleotide-mediated transformation allowed low levels of abasic-site bypass to be observed in S. acidocaldarius and demonstrated that the local sequence context affected bypass specificity; in addition, most erroneous TLS did not require Dbh function. Applying the technique to another common lesion, 7,8-dihydro-8-oxo-deoxyguanosine (8-oxo-dG), revealed an antimutagenic role of Dbh. The efficiency and accuracy of replication past 8-oxo-dG was higher in the presence of Dbh, and up to 90% of the Dbh-dependent events inserted dC. A third set of assays, based on phenotypic reversion, showed no effect of Dbh function on spontaneous −1 frameshifts in mononucleotide tracts in vivo, despite the extremely frequent slippage at these motifs documented in vitro. Taken together, the results indicate that a primary genetic role of Dbh is to avoid mutations at 8-oxo-dG that occur when other Sulfolobus enzymes replicate past this lesion. The genetic evidence that Dbh is recruited to 8-oxo-dG raises questions regarding the mechanism of recruitment, since Sulfolobus spp. have eukaryotic-like replisomes but no ubiquitin.     

Responses of Vegetable Seeds to Controlled Hydration

Leek, onion and carrot seeds were imbibed in water and in solutionsof polyethylene glycol (PEG) 6000 over the range –0.5to –4.0 MPa osmotic potential, for periods up to 28 dat 15 C. Seeds started to germinate after 7 and 14 d at –0.5MPa and –1.0 MPa PEG, respectively, but in the lattercase, germination did not exceed 5%. No germination occurredin solutions of lower (more negative) osmotic potential. Seedmoisture content increased with osmotic potential in all threespecies and the relationships were unaffected by the durationof imbibition in solutions of –1.0 to –4.0 MPa,though leek seeds had higher moisture contents than the otherspecies for any given osmotic potential. Linear relationships between response to priming (differencebetween mean germination times of primed and untreated seeds)and seed moisture content were obtained for each species, positiveresponses being obtained above 30–35% seed moisture contentwith optima at 46, 44.5 and 44% seed moisture contents in leek,onion and carrot, respectively. Priming had no effect on embryovolume or cell number per embryo in leek and onion. Carrot embryovolume increased by 43% and cell number per embryo doubled inprimed compared with untreated seeds, whereas seeds imbibedin water showed only a slight increase in cell number per embryoat the stage when radicles were beginning to penetrate the seedcoat. Allium cepa L. cv. Rijnsburger Robusta, onion, Allium porrum L. cv. Winterreuzen, leek, Daucus carota L. cv. Nantaise, carrot, germination, priming, polyethylene glycol, seed moisture, cell number, embryo volume     

The effects of salinity and osmotic stress on barley germination rate: sodium as an osmotic regulator

Background and Aims

Seed germination is negatively affected by salinity, which is thought to be due to both osmotic and ion-toxicity effects. We hypothesize that salt is absorbed by seeds, allowing them to generate additional osmotic potential, and to germinate in conditions under which they would otherwise not be able to germinate.

Methods

Seeds of barley, Hordeum vulgare, were germinated in the presence of either pure water or one of five iso-osmotic solutions of polyethylene-glycol (PEG) or NaCl at 5, 12, 20 or 27 °C. Germination time courses were recorded and germination indices were calculated. Dry mass, water content and sodium concentration of germinating and non-germinating seeds in the NaCl treatments at 12 °C were measured. Fifty supplemental seeds were used to evaluate the changes in seed properties with time.

Key Results

Seeds incubated in saline conditions were able to germinate at lower osmotic potentials than those incubated in iso-osmotic PEG solutions and generally germinated faster. A positive correlation existed between external salinity and seed salt content in the saline-incubated seeds. Water content and sodium concentration increased with time for seeds incubated in NaCl. At higher temperatures, germination percentage and dry mass decreased whereas germination index and sodium concentration increased.

Conclusions

The results suggest that barley seeds can take up sodium, allowing them to generate additional osmotic potential, absorb more water and germinate more rapidly in environments of lower water potential. This may have ecological implications, allowing halophytic species and varieties to out-compete glycophytes in saline soils.     

Global 5-methylcytosine alterations in DNA during ageing of Quercus robur seeds

Background and Aims Epigenetic regulation plays an important role in the management of plant growth, development and response to stress factors, and several reports have indicated that DNA methylation plays a critical role in seed development and viability. This study examines changes in 5-methylcytosine (m⁵C) levels in the DNA of seeds during ageing, a process that has important implications for plant conservation and agriculture.Methods Changes in the global level of m⁵C were measured in mature seeds of oak, Quercus robur. The extent of DNA methylation was measured using a protocol based on two-dimensional thin-layer chromatography. Viability of seeds was determined by germination and seedling emergence tests.Key Results An ageing-related decrease in total m⁵C during storage of recalcitrant seeds was highly and significantly correlated with a decrease in seed viability, as reflected by a reduction in germination (r = 0·8880) and seedling emergence (r = 0·8269).Conclusions The decrease in viability during ageing of Q. robur seeds is highly correlated with a global decline in the amount of m⁵C in genomic DNA, and it is possible that this may represent a typical response to ageing and senescence in recalcitrant seeds. Potential mechanisms that drive changes in genomic DNA methylation during ageing are discussed, together with their implications for seed viability.     

The Importance of Genetically Determined Seed Coat Characteristics to Seed Quality in Grain Legumes

Comparisons of five pairs of isogenk lines of peas, differingonly in the A gene for seed coat colour showed that white seeds(genotype aa) imbibed more rapidly than coloured seeds (AA),suffered greater imbibition damage revealed by dead tissue onthe cotyledons, and higher solute leakage. Seed-coat pigmentationwas closely associated with slow water uptake, since when expressionof the A gene was suppressed by the recessive pollens gene,the resulting white seeds {palpal AA) imbibed rapidly. The slowwater uptake by coloured seeds was not due to the restrictionof water entry by the seed coat since the differences in imbibitionrate were maintained when a portion of the seed coat was removedand seeds were imbibed with the exposed cotyledon in contactwith moist filter paper. Imbibition of similarly treated seedsby immersion in polyethylene glycol solutions (1–4%) whichincreased the seed/solution wettability, had little effect onthe water uptake of coloured seeds compared to imbibition inwater whereas that of white seeds increased in the first 10mins imbibition. Poor wettability of the inner surface of colouredseed coats did not therefore explain the slow imbibition ofthese seeds. The white seed coats loosened rapidly during imbibitionwhilst the coloured seed coats remained closely associated withthe cotyledons suggesting that the adherence of the seed coatto the cotyledons and therefore the ease of access of waterbetween the testa and cotyledons determines the rate of imbibition.The rapid water uptake by white-coated seeds and the subsequentimbibition damage may explain the high incidence of infectionof these seeds by the soil-bome fungus Pythhan after 2 d insoil. Improved seed quality and emergence may therefore be achievedby breeding for seed coat characteristics leading to reducedrates of imbibition Pisum sativum, isogenic lines, A gene, seed coat colour, imbibition, imbibition damage, wettability, pollens gene, seed quality, grain legumes     

Enhanced osmotic stress tolerance in Medicago truncatula plants overexpressing the DNA repair gene MtTdp2α (tyrosyl-DNA phosphodiesterase 2)

No information is currently available in plants concerning the tyrosyl-DNA phosphodiesterase 2 (Tdp2) enzyme which in animals is involved in the removal of DNA topoisomerase II-mediated DNA damage and cell proliferation/differentiation signaling. Bioinformatic investigation revealed the occurrence in the plant kingdom of three distinct Tdp2 isoforms, named α, β and γ. The MtTdp2α gene from Medicago truncatula Gaertn., encoding a protein with putative nuclear localization signal and chloroplast transit peptide, was significantly up-regulated in response to osmotic stress induced by polyethylene glycol. The transgenic M. truncatula lines Tdp2α-13C and Tdp2α-28 overexpressing the MtTdp2α gene were characterised by enhanced tolerance to both osmotic and photo-oxidative stress. According to single cell gel electrophoresis, MtTdp2α gene overexpression prevented accumulation of double strand breaks in absence and presence of osmotic stress. Interestingly, the MtMRE11, MtRAD50 and MtNBS1 genes involved in double strand break sensing/repair were significantly up-regulated in the MtTdp2α-overexpressing plants grown under physiological conditions and no further up-regulation occurred in response the osmotic agent. The Tdp2α-13C and Tdp2α-28 lines also showed significant up-regulation of several genes essential for the control of DNA topology and genome maintenance, such as MtTdp1α, MtTop2 (DNA topoisomerase II) and MtGYR (DNA gyrase). The role of MtTdp2α gene in enhancing the plant response to genotoxic injury under osmotic stress is discussed.     

Molecular cloning and expression analysis of the sucrose transporter gene family from Theobroma cacao L.

In this study, we performed cloning and expression analysis of six putative sucrose transporter genes, designated TcSUT1, TcSUT2, TcSUT3, TcSUT4, TcSUT5 and TcSUT6, from the cacao genotype ‘TAS-R8’. The combination of cDNA and genomic DNA sequences revealed that the cacao SUT genes contained exon numbers ranging from 1 to 14. The average molecular mass of all six deduced proteins was approximately 56 kDa (range 52 to 66 kDa). All six proteins were predicted to exhibit typical features of sucrose transporters with 12 trans-membrane spanning domains. Phylogenetic analysis revealed that TcSUT2 and TcSUT4 belonged to Group 2 SUT and Group 4 SUT, respectively, and the other TcSUT proteins were belonging to Group 1 SUT. Real-time PCR was conducted to investigate the expression pattern of each member of the SUT family in cacao. Our experiment showed that TcSUT1 was expressed dominantly in pods and that, TcSUT3 and TcSUT4 were highly expressed in both pods and in bark with phloem. Within pods, TcSUT1 and TcSUT4 were expressed more in the seed coat and seed from the pod enlargement stage to the ripening stage. TcSUT5 expression sharply increased to its highest expression level in the seed coat during the ripening stage. Expression pattern analysis indicated that TcSUT genes may be associated with photoassimilate transport into developing seeds and may, therefore, have an impact on seed production.     

Changes in Some ATP-Dependent Activities in Seeds during Treatment with Polyethyleneglycol and during the Redrying Process

During the imbibition of seeds in polyethyleneglycol (PEG),increasing amounts of ATP accumulated up to 24 h. Similar amountsaccumulated in the seeds during 4–5 h of imbibition inwater. Radioactive amino acids were increasingly incorporatedin the acid-insoluble fraction up to 24 h imbibition in PEG,as well as in water, after which a sharp decrease occurred upto 5 d of imbibition. If seeds were imbibed in PEG or waterin the presence of radioactive acetate, water-insoluble radioactivityincreased linearly in seeds during 5 d of imbibition. The amountsof incorporated amino acids or acetate were about double inPEG-imbibed as compared with in water-imbibed seed. The incorporationof AMP into the acid-insoluble fraction in seeds imbibed inPEG in the presence of radioactive AMP levelled off after 24h followed by a sharp decrease of up to 10% of the peak 5 dafter the start of imbibition. In water-imbibed seeds the incorporationof AMP continued to increase during at least 5 d of imbibition.During redrying of PEG-treated seeds (24 h), at least 80% ofthe accumulated ATP decreased during 18 d. The total radioactiveamino acids and nucleotide decreased during 3 d of redryingby 20% and 60%, respectively. At that time, the acid-insolubleincorporates increased by 20% and 50%, respectively. Some ofthe AMP was released as CO₂. Key words: AMP, Germination, Nucleic acid synthesis, Osmoconditioning, PEG, Protein synthesis     

Gamma irradiation with different dose rates induces different DNA damage responses in Petunia x hybrida cells

In plants, there is evidence that different dose rate exposures to gamma (γ) rays can cause different biological effects. The dynamics of DNA damage accumulation and molecular mechanisms that regulate recovery from radiation injury as a function of dose rate are poorly explored. To highlight dose-rate dependent differences in DNA damage, single cell gel electrophoresis was carried out on regenerating Petunia x hybrida leaf discs exposed to LDR (total dose 50 Gy, delivered at 0.33 Gy min⁻¹) and HDR (total doses 50 and 100 Gy, delivered at 5.15 Gy min⁻¹) γ-ray in the 0–24 h time period after treatments. Significant fluctuations of double strand breaks and different repair capacities were observed between treatments in the 0–4 h time period following irradiation. Dose-rate-dependent changes in the expression of the PhMT2 and PhAPX genes encoding a type 2 metallothionein and the cytosolic isoform of ascorbate peroxidase, respectively, were detected by Quantitative RealTime-Polymerase Chain Reaction. The PhMT2 and PhAPX genes were significantly up-regulated (3.0- and 0.7-fold) in response to HDR. The results are discussed in light of the potential practical applications of LDR-based treatments in mutation breeding.     

Cold stratification,light and high seed density enhance the germination of Ottelia alismoides

The effects of cold stratification, light and seed clustering in petri dish on Ottelia alismoides seed germination were investigated. The seeds required light and an extended cold period in order to germinate, but neither treatment alone was effective. Seed germination significantly increased with length of the 4 °C cold stratification period. Freshly collected seeds failed to germinate while a 5-month period at 4 °C yielded 29 ± 9% germination in the light, but none in the dark. Treatment with sodium nitroprusside, a nitric oxide source, failed to promote germination in the light or dark. Seeds of O. alismoides showed an unusual and significant positive response to aggregation. Germination in the light, after 5-month 4 °C cold stratification, was stimulated to almost five-fold in the dishes that were more densely sown with seed (20 seeds versus 200 seeds). Likewise, clustering seeds in dense aggregations stimulated germination significantly. Germination more than quadrupled with an increase from 1 to 50 seeds per cluster (200 seeds per dish), reaching a value of 72 ± 4%. Linear regression analysis shows the correlation between seed cluster density (no. per cluster) and germination rate (%) was highly significant (R² = 0.85, P = 0.000). The extended cold stratification requirement is probably an over-wintering device. The mechanism of the density-dependent stimulation is unclear.     

The roles of inorganic nitrogen salts in maintaining phytochrome- and gibberellin A3-mediated germination control in skotodormant lettuce seeds

Skotodormant seeds of Lactuca sativa Grand Rapids imbibed in darkness for 10 days (10-day DS) germinated poorly upon terminal treatment with red light (R) or gibberellin A₃ (GA₃). Inorganic nitrogen salts in the imbibition solutions reduced seed skotodormancy. Ten-day DS seeds, imbibed in 25 mm salt solutions followed by terminal R, germinated 99% if imbibed in NH₄NO₃, 70% if imbibed in KNO₃ or NH₄Cl, and 55% if imbibed in NaNO₃. Seeds imbibed in higher salt concentrations germinated fully upon terminal R treatment. Seeds imbibed in 25 mm NH₄Cl or in 50 mm NH₄NO₃ germinated completely upon GA₃ treatment. Osmotic effects of imbibition media accounted for only part of the effect, since seeds imbibed in 50 mm CaCl₂ or NaCl germinated poorly following R or GA₃ treatment. Seeds imbibed in 500 mm polyethylene glycol (PEG) 1000 or mannitol solutions for 10 days still exhibited skotodormancy. Treatments of R or GA₃ did not stimulate germination in seeds imbibed in mannitol, but germination was complete if seeds were given 1-h acid immersion plus a water rinse before the terminal R or GA₃ treatment. Seeds imbibed in 50–500 mm PEG during 10-day DS germinated significantly better in response to terminal R. Terminal GA₃ significantly improved germination only in seeds imbibed at 500 mm PEG. P_fr appeared to function in mannitol-imbibed seed only after an acid treatment. Seed exposure to inorganic nitrogen salts during the 10-day DS maintained seed sensitivity to terminal R or GA₃ treatment. The depth of seed skotodormancy was related to the availability of inorganic nitrogen and also involved the levels of P_fr or endogenous GA₃.Abbreviations FR far red - DS dark storage - R red - GA₃ gibberellin A₃ - PEG polyethylene glycol - SHAM salicylhydroxamic acid - ANOVA analysis of variance - GLM general linear model - LSD least squares difference - P_fr far-red absorbing form of phytochrome     

Seed orientation and magnetic field strength have more influence on tomato seed performance than relative humidity and duration of exposure to non-uniform static magnetic fields

Different factors (e.g., light, humidity, and temperature) including exposure to static magnetic fields (SMFs), referred here as critical factors, can significantly affect horticultural seed performance. However, the link between magnetic field parameters and other interdependent factors affecting seed viability is unclear. The importance of these critical factors affecting tomato (Solanum lycopersicum L.) var. MST/32 seed performance was assessed after performing several treatments based on a L₉ (3⁴) (four factors at three levels) orthogonal array (OA) design. The variable factors in the design were magnetic flux density (R₁ = 332.1 ± 37.8 mT; R₂ = 108.7 ± 26.9 mT; and R₃ = 50.6 ± 10.5 mT), exposure time (1, 2, and 24 h), seed orientation (North polarity, South polarity, and control – no magnetic field), and relative humidity (RH) (7.0, 25.5, and 75.5%). After seed moisture content stabilisation at the different chosen RH, seeds were exposed in dark under laboratory conditions to several treatments based on the OA design before performance evaluation. Treatments not employing magnetic field exposure were used as controls. Results indicate that electrolyte leakage rate was reduced by a factor of 1.62 times during seed imbibition when non-uniform SMFs were employed. Higher germination (∼11.0%) was observed in magnetically-exposed seeds than in non-exposed ones, although seedlings emerging from SMF treatments did not show a consistent increase in biomass accumulation. The respective influence of the four critical factors tested on seed performance was ranked (in decreasing order) as seed orientation to external magnetic fields, magnetic field strength, RH, and exposure time. This study suggests a significant effect of non-uniform SMFs on seed performance with respect to RH, and more pronounced effects are observed during seed imbibition rather than during later developmental stages.     

Mechanism of seed priming in circumventing thermodormancy in lettuce

Lettuce (Lactuca sativa L. cv Minetto) seeds were primed in aerated solutions of 1% K₃PO₄ or water at 15°C in the dark for various periods of time to determine the manner by which seed priming bypasses thermodormancy. Seeds which were not primed did not germinate at 35°C, whereas those which were primed for 20 h in 1% K₃PO₄ or distilled H₂O had up to 86% germination. The rate of water uptake and respiration during priming were similar regardless of soak solution. Cell elongation occurred in both water and 1% K₃PO₄, 4 to 6 h prior to cell division. Both processes commenced sooner in water than K₃PO₄. Radicle protrusion (germination) occurred in the priming solution at 21 h in water and 27 h in 1% K₃PO₄.

Respiration, radicle protrusion and cell division consistently occurred sooner in primed (redried) seeds compared to nonprimed seeds when they were imbibed at 25°C. Cell division and elongation commenced after 10 h imbibition in primed (redried) seeds imbibed at 35°C. Neither process occurred in nonprimed seeds. Respiratory rates were higher in both primed and nonprimed seeds imbibed at 35°C compared to those imbibed at 25°C, although radicle protrusion did not occur in nonprimed seeds which were imbibed at 35°C. It is apparent that cell elongation and division are inhibited during high temperature imbibition in nonprimed lettuce seeds. Seed priming appears to lead to the irreversible initiation of cell elongation, thus overcoming thermodormancy.

     

Characterization of the complete mitochondrial genome of Tryporyza incertulas, in comparison with seven other Pyraloidea moths

The complete 15,223-bp mitochondrial genome (mitogenome) of Tryporyza incertulas (Walker) (Lepidoptera: Pyraloidea: Crambidae) was determined, characterized and compared with seven other species of superfamily Pyraloidea. The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. Compared with other moths of Pyraloidea, the A + T biased (77.0%) of T. incertulas was the lowest. Eleven protein-coding genes (PCGs) utilized the standard ATN, but cox1 used CGA and nad4 used AAT as the initiation codons. Ten protein-coding genes had the common stop codon TAA, except nad3 having TAG as the stop codon, and cox2, nad4 using T, TA as the incomplete stop codons, respectively. All of the tRNA genes had typical cloverleaf secondary structures except trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. There was a spacer between trnQ and nad2, which was common in Lepidoptera moths. A 6-bp motif ‘ATACTA’ between trnS2(UCN) and nad1, a 7-bp motif “AGC(T)CTTA” between trnW and trnC and a 6-bp motif “ATGATA” of overlapping region between atp8 and atp6 were found in Pyraloidea moths. The A + T-rich region contained an ‘ATAGT(A)’-like motif followed by a poly-T stretch. In addition, two potential stem-loop structures, a duplicated 19-bp repeat element, and two microsatellites ‘(TA)₁₂’ and ‘(TA)₉’ were observed in the A + T-rich region of T. incertulas mitogenome. Finally, the phylogenetic relationships of Pyraloidea species were constructed based on amino acid sequences of 13 PCGs of mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. These molecular-based phylogenies supported the morphological classification on relationships within Pyraloidea species.     

A unique tRNA gene family and a novel,highly expressed ORF in the mitochondrial genome of the silver-lip pearl oyster, Pinctada maxima (Bivalvia: Pteriidae)

Characteristics of mitochondrial (mt) DNA such as gene content and arrangement, as well as mt tRNA secondary structure, are frequently used in comparative genomic analyses because they provide valuable phylogenetic information. However, most analyses do not characterize the relationship of tRNA genes from the same mt genome and, in some cases, analyses overlook possible novel open reading frames (ORFs) when the 13 expected protein-coding genes are already annotated. In this study, we describe the sequence and characterization of the complete mt genome of the silver-lip pearl oyster, Pinctada maxima. The 16,994-bp mt genome contains the same 13 protein-coding genes (PCGs) and two ribosomal RNA genes typical of metazoans. The gene arrangement, however, is completely distinct from that of all other available bivalve mt genomes, and a unique tRNA gene family is observed in this genome. The unique tRNA gene family includes two trnS^− AGY and trnQ genes, a trnM isomerism, but it lacks trnS^− CUN. We also report the first clear evidence of alloacceptor tRNA gene recruitment (trnP → trnS^− AGY) in mollusks. In addition, a novel ORF (orfUR1) expressed at high levels is present in the mt genome of this pearl oyster. This gene contains a conserved domain, “Oxidored_q1_N”, which is a member of Complex I and thus may play an important role in key biological functions. Because orfUR1 has a very similar nucleotide composition and codon bias to that of other genes in this genome, we hypothesize that this gene may have been moved to the mt genome via gene transfer from the nuclear genome at an early stage of speciation of P. maxima, or it may have evolved as a result of gene duplication, followed by rapid sequence divergence. Lastly, a 319-bp region was identified as the possible control region (CR) even though it does not correspond to the longest non-coding region in the genome. Unlike other studies of mt genomes, this study compares the evolutionary patterns of all available bivalve mt tRNA and atp8 genes.