Species Of Fagaceae Research Articles

Diminishing returns: A comparison between fresh mass vs. area and dry mass vs. area in deciduous species.

“Diminishing returns” in leaf economics occurs when increases in lamina mass (M), which can either be represented by lamina dry mass (DM) or fresh mass (FM), fail to produce proportional increases in leaf surface area (A), such that the scaling exponent (α) for the M vs. A scaling relationship exceeds unity (i.e., α > 1.0). Prior studies have shown that FM vs. A is better than DM vs A in assessing diminishing returns in evergreen species. However, the superiority of FM vs. A over DM vs. A has been less well examined for deciduous species. Here, we applied reduced major axis protocols to test whether FM vs. A is better than DM vs. A to describe the M vs. A scaling relationship, using a total of 4271 leaves from ten deciduous and two evergreen tree species in the Fagaceae and Ulmaceae for comparison. The significance of the difference between the scaling exponents of FM vs. A and DM vs. A was tested using the bootstrap percentile method. Further, we tested the non-linearity of the FM (DM) vs. A data on a log-log scale using ordinary least squares. We found that (i) the majority of scaling exponents of FM vs. A and DM vs. A were >1 thereby confirming diminishing returns for all 12 species, (ii) FM vs. A was more robust than DM vs. A to identify the M vs. A scaling relationship, (iii) the non-linearity of the allometric model was significant for both DM vs. A and FM vs. A., and (iv) the evergreen species of Fagaceae had significantly higher DM and FM per unit area than other deciduous species. In summary, FM vs. A is a more reliable measure than DM vs. A when dealing with diminishing returns, and deciduous species tend to invest less biomass in unit leaf light harvesting area than evergreen species.

A New Species of Lithocarpus (Fagaceae) from Ca Dam Mountain of Quang Ngai Province, Vietnam

Abstract— Lithocarpus cadamensis Ngoc & Son, a new species of Fagaceae, is described and illustrated from Mt. Ca Dam, Tra Bong District, Quang Ngai Province, central Vietnam. The new species is characterized by its large leaf blades with long petioles, solitary and subsessile cupules which almost completely cover the nut, and spiny cupule scales, in a combination that clearly differs from the previously known species of Lithocarpus including the most similar species in the region, L. campylolepis, L. eucalyptifolius, and L. gougerotae. A MIG-seq phylogeny based on genome-wide SNPs reveals a phylogenetic position close to L. eucalyptifolius, from which the new species is differentiated by multiple morphological characters. A morphological description and comparison with related species, photographs, line drawing, preliminary conservation status, and DNA barcode sequences are provided for the new species.

New Fagaceous pollen taxa from the Miocene Søby flora of Denmark and their biogeographic implications.

The Fagaceae comprise around 1000 tree species in the Northern Hemisphere. Despite an extensive fossil pollen record, reconstructing biogeographic patterns is hampered because it is difficult to achieve good taxonomic resolution with light microscopy alone. We investigate dispersed pollen of Fagaceae from the Miocene Søby flora, Denmark. We explore the latitudinal gradient in Fagaceae distribution during the Miocene Climatic Optimum (MCO) in Europe and the Northern Hemisphere to compare it with the Eocene Warmhouse and the present. We investigated dispersed pollen using light and scanning electron microscopy. We assessed biogeographic patterns in Fagaceae during two warm periods in Earth history (MCO, Eocene) and the present. Eight species of Fagaceae were recognized in the Søby flora. Of these, Fagus had a continuous Mediterranean to subarctic distribution during MCO; Quercus sect. Cerris and castaneoids had northern limits in Denmark, and evergreen Quercus sect. Ilex in Central Europe. In a northern hemispheric context, Fagus and sections of Quercus had more northerly distribution limits during Eocene and MCO with maximum northward extensions during Eocene (Fagus, castaneoids) or Oligo-Miocene (Quercus sects. Cerris and Ilex). The known distribution of the extinct Tricolporopollenites theacoides during MCO included Central Europe and East China, while this taxon thrived in South China during Eocene. More northerly distributions during MCO and Eocene probably were determined by temperature. In contrast, fossil occurrences in areas that are arid or semi-humid today were determined by maritime conditions in these areas (western North America, Central Asia) during the Cenozoic.

Production of Doubled Haploid Embryos from Cork Oak Anther Cultures by Antimitotic Agents and Temperature Stress.

Cork oak (Quercus suber L.) is a forest tree species of the family Fagaceae. It is characterized by long life cycles which hamper doubled haploid plant production to obtain homozygotes and pure lines. The time-consuming method of repeated backcrossings by conventional breeding techniques to produce pure lines is impractical in woody species. Nevertheless, biotechnology has offered new tools to make it possible. A doubled haploid plant or embryo is one that is developed by the doubling of a haploid set of chromosomes. A protocol to produce doubled haploids of cork oak has been developed through microspore embryogenesis. By a heat stress treatment, the microspores inside the anther leave the gametophytic pathway and react shifting their development to the sporophytic pathway by means of which haploid embryos are obtained. Chromosome duplication of haploids from cork oak anther cultures occurs either spontaneously or may be induced by the application of antimitotic agents (e.g., colchicine, oryzalin, amiprophos-methyl). Furthermore, a genetic test is designed through microsatellite markers to elucidate whether the diploid embryos obtained are originally haploids which spontaneously duplicated their genome, or alternatively those embryos are generated from the diploid tissue of the anther wall. Here we describe a detailed protocol to produce doubled haploid individuals from cork oak anther cultures by using temperature stress and antimitotic agents.

Fruit development of Lithocarpus (Fagaceae) and the role of heterochrony in their evolution.

Stone oaks, or Lithocarpus species of Fagaceae are ecologically important canopy trees in the tropical and subtropical forests over East Asia, and the fruits of which are important food sources for insects and vertebrates there. The great fruit morphological variation of thisgenus represents two fruit types, acorn and enclosed receptacle fruit types. However, the evolutionary mechanisms of differentiation into these two fruit types with contrasting morphology remain a puzzle. To reveal the morphogenetic properties of two fruit types, we observed tissue differentiation and development among 20 Lithocarpus species from fruit set to maturity. Unlike in fruits of Quercus, the endocarp differentiation in Lithocarpus fruits occurred later than exocarp and mesocarp. Cupules provided further protection of developing seeds, particularly of acorn-type fruits. Fruits of Lithocarpus and Quercus acorns share similar insect predators. At fruit set, both acorn and enclosed receptacle types were largely identical, with similar tissue morphology and the sequence of differentiation. The distinct difference between two fruit types at maturity came from varied rates and degrees of development between the pericarp and receptacle tissues. We found that heterochrony between two tissues could create substantially divergent ecological strategies for protection and dispersal of their seeds, which is essential for the evolution of two fruit types.

Coordination of leaf and stem traits in 25 species of Fagaceae from three biomes of East Asia

It has been debated whether leaf and stem economics spectra are coordinated across species, because previous studies have provided contradictory results. These studies have been restricted to single biomes, and we hypothesize that climate seasonality may determine the strength of coordination between leaf and stem trait combinations. Herein, using 25 Fagaceae species from East Asia, we investigated the coordination of 16 leaf traits and 5 stem traits across and within three biomes (cool temperate, warm temperate, and tropical forests). The traits were chosen to reflect multiple aspects of plant adaptive strategies, such as water, carbon, and nutrient use. The leaf and stem traits of species that reflect resource-use strategies for different resources were functionally coordinated, forming a single axis of trait variation across biomes. This axis represents the trade-off between fast and slow resource-use strategies. We found the trend that the coordination between leaf and stem traits was the strongest in cool temperate forests after removing two Fagus species, followed by warm temperate forests, but was not observed in tropical forests. Our results support the proposed model that plants vary from slow to fast resource exploitation, using closely related species, and suggest that temperature modulates the coordination of leaf and stem economics spectra.

Studies on the Evergreen Broad-leaved Forests of Yunnan, Southwestern China

Yunnan of southwestern China supports an extremely rich biodiversity and various vegetation types dominated by evergreen broad-leaved forest. The floristic composition, species diversity, physiognomy and biogeography of three major types of the evergreen broad-leaved forest in Yunnan were surveyed using 1-ha plots. The three forest types are very diverse in species composition, diversity, physiognomy and biogeography, although they are commonly dominated by species of the families Fagaceae, Theaceae and Lauraceae. The lower montane evergreen broad-leaved forest (LMEB) in southern Yunnan is extremely rich in species and is characterized by a tropical physiognomy and dominated by tropical Asian species, similar to the tropical lower montane evergreen forest commonly in southeast Asia. The semi-wet evergreen broad-leaved forest (SWEB) on plateaus and the upper montane evergreen broad-leaved forest (UMEB) in central and northern Yunnan are characterized by a subtropical physiognomy and are dominated by Sino-Himalayan and Chinese endemic species, and are unique in southwestern China. The SWEB and the UMEB should be given high conservation values due to their uniqueness and abundant Chinese endemic species. Especially, the SWEB should be given the highest protection because most remnants of this forest have lost due to heavily human disturbance.

Is there a substitution of Pinaceae by Fagaceae in temperate forests at the global scale?

Abstract Reports on forest decline, changes in species composition and the distribution of forests in response to changes in climate and land use are increasing worldwide. Temperate forests are largely dominated by two tree families: Pinaceae and Fagaceae. These two families have distinct functional properties and different responses to environmental factors. Several local and regional assessments, particularly in Europe, have found that species of Fagaceae are invading areas previously dominated by Pinaceae. The main aim of this synthesis study is to analyze the relative dynamics of Pinaceae and Fagaceae species in temperate forests around the world, with the following specific objectives: (1) establish if there is a consistent directional substitution of Pinaceae by Fagaceae worldwide; and (2) determine whether these directional changes are associated with specific climatic conditions or certain geographic regions, reflecting differences in historical forest management and land use. A bibliographic review was performed and 51 papers were found that met the search criteria, including a total of 121 case studies in which the relative dynamics of Pinaceae and Fagaceae were evaluated. Our results show that the relative abundance of Fagaceae increased in 71% of cases (P → F dynamics), whereas Pinaceae relative abundance increased in 17% of cases (F → P) and 12% of cases did not show clear changes. Increases of Fagaceae relative to Pinaceae were less clear in areas where vegetation dynamics were driven by natural disturbances. Our results indicate a widespread increase in dominance of Fagaceae species at the expense of Pinaceae across northern temperate forests, with the exception of Eastern North America. The potential implications for ecosystem function and forest resilience under ongoing climate change are large and clearly deserve further study.

Distribution and diversity of Fagaceae in Hidalgo, Mexico

Background: The family Fagaceae is one of the most important in temperate regions of the Northern hemisphere. Fagus and Quercus are distributed in Mexico, the former in Northeastern Mexico, while the latter reaches a high diversity in the Sierra Madre Oriental, Mexico. In Hidalgo state, located mainly in the Sierra Madre Oriental, knowledge of the Fagaceae diversity is still uncertain.
 Questions and/or hypothesis: We carried out a taxonomic revision of the genus and species of Fagaceae in Hidalgo state. We determined how many and which species are distributed in Hidalgo. We also present a morphological description and ecological characters of each one.
 Studied species: The species of the family Fagaceae
 Study site: Hidalgo state, Mexico.
 Method: We collected herbarium specimens, made field observations and reviewed herbarium data of Fagaceae specimens at FCME, INEGI, MEXU, ENCB, SLPM, HUMO, XAL and partly BH herbaria. In addition, we checked taxonomic literature and protologues of each species.
 Results: We found one species of Fagus and 43 of Quercus , 22 of which belong to the section Quercus (white oaks) and 21 to section Lobatae (red oaks). Morphological descriptions, altitudinal and geographical distribution, vegetation types of each species and a dichotomous key for species identification are presented. Illustrations and photographs of the species are also included.
 Conclusions: A high diversity of Fagaceae species is present in Hidalgo state. In Mexico, Hidalgo ranks in fifth place for oak species diversity, just behind Oaxaca (50 species), Puebla (50), San Luis Potosí (45), and Jalisco (45).

Distribution Patterns and Long-Term Changes in Vascular Plants of Non-Littoral Areas in the SW Archipelago of Finland. Part II. Pinaceae, Cupressaceae, Nymphaeaceae, Ranunculaceae, Papaveraceae, Ulmaceae, Cannabaceae, Urticaceae, Fagaceae, Betulaceae, Myricaceae, Caryophyllaceae, Chenopodiaceae, Polygonaceae

Historical (mainly 1930s) and contemporary records of 482 vascular plant species or genus of non-littoral areas of 464 islands in the archipelago of SW Finland are compared to visualise changes in distribution patterns, and to identify environmental variables that exert an influence on the distribution of the species. The environmental variables were measured in a GIS. Logistic regression analysis was used to find variables that exert an influence on the probability of species occurrences. In this second part of a series of papers results, including distribution maps, are presented for species of Pinaceae, Cupressaceae, Nymphaeaceae, Ranunculaceae, Papaveraceae, Ulmaceae, Cannabaceae, Urticaceae, Fagaceae, Betulaceae, Myricaceae, Caryophyllaceae, Chenopodiaceae and Polygonaceae. A synthesis of the study will be presented in the last part of this article series.

Evaluation of forest structure, biomass and carbon sequestration in subtropical pristine forests of SW China.

Very old natural forests comprising the species of Fagaceae (Lithocarpus xylocarpus, Castanopsis wattii, Lithocarpus hancei) have been prevailing since years in the Ailaoshan Mountain Nature Reserve (AMNR) SW China. Within these forest trees, density is quite variable. We studied the forest structure, stand dynamics and carbon density at two different sites to know the main factors which drives carbon sequestration process in old forests by considering the following questions: How much is the carbon density in these forest trees of different DBH (diameter at breast height)? How much carbon potential possessed by dominant species of these forests? How vegetation carbon is distributed in these forests? Which species shows high carbon sequestration? What are the physiochemical properties of soil in these forests? Five-year (2005-2010) tree growth data from permanently established plots in the AMNR was analysed for species composition, density, stem diameter (DBH), height and carbon (C) density both in aboveground and belowground vegetation biomass. Our study indicated that among two comparative sites, overall 54 species of 16 different families were present. The stem density, height, C density and soil properties varied significantly with time among the sites showing uneven distribution across the forests. Among the dominant species, L. xylocarpus represents 30% of the total carbon on site 1 while C. wattii represents 50% of the total carbon on site 2. The average C density ranged from 176.35 to 243.97tCha-1. The study emphasized that there is generous degree to expand the carbon stocking in this AMNR through scientific management gearing towards conservation of old trees and planting of potentially high carbon sequestering species on good site quality areas.

Monitoring of plant–environment interactions by high‐throughput FTIR spectroscopy of pollen

Summary Fourier transform infrared (FTIR) spectroscopy enables chemical analysis of pollen samples for plant phenotyping to study plant–environment interactions, such as influence of climate change or pathogens. However, current approach, such as microspectroscopy and attenuated total reflection spectroscopy, does not allow for high‐throughput protocols. This study at hand suggests a new spectroscopic method for high‐throughput characterization of pollen. Samples were measured as thin films of pollen fragments using a Bruker FTIR spectrometer with a high‐throughput eXTension (HTS‐XT) unit employing 384‐well plates. In total, 146 pollen samples, belonging to 31 different pollen species of Fagaceae and Betulaceae and collected during three consecutive years (2012–2014) at locations in Croatia, Germany and Norway, were analysed. Critical steps in the sample preparation and measurement, such as variabilities between technical replicates, between microplates and between spectrometers, were studied. Measurement variations due to sample preparation, microplate holders and instrumentation were low, and thus allowed differentiation of samples with respect to phylogeny and biogeography. The spectral variability for a range of Fagales species (Fagus, Quercus, Betula, Corylus, Alnus and Ostrya) showed high‐species‐specific differences in pollen's chemical composition due to either location or year. Statistically significant inter‐annual and locational differences in the pollen spectra indicate that pollen chemical composition has high phenotypic plasticity and is influenced by local climate conditions. The variations in composition are connected to lipids, proteins, carbohydrates and sporopollenins that play crucial roles in cold and desiccation tolerance, protection against UV radiation and as material and energy reserves. The results of this study demonstrate the value of high‐throughput FTIR approach for the systematic collection of data on ecosystems. The novel FTIR approach offers fast, reliable and economical screening of large number of samples by semi‐automated methodology. The high‐throughput approach could provide crucial understanding on plant–climate interactions with respect to biochemical variation within genera, species and populations.

Review of Parathoracaphis Takahashi, 1958 with description of a new species from China (Hemiptera, Aphididae, Hormaphidinae).

The aphid genus Parathoracaphis Takahashi, 1958 is reviewed. Parathoracaphis spinapilosa sp. n., found on Quercus sp. and on an unidentified species of Fagaceae in China is described and illustrated. A generic diagnosis and a key to Parathoracaphis species are presented.

Sporogenesis and gametogenesis in Chinese chinquapin (Castanea henryi (Skam) Rehder & Wilson) and their systematic implications

We provide new embryological information regarding the Fagaceae family. Abortive ovules may be a result of mate choice and be necessary to maximize reproductive success in Chinese chinquapin ( Castanea henryi ). In contrast to most angiosperms, in which fertilization occurs 1–2 days after pollination, fertilization in Fagales is delayed from 4 days to more than 1 year. However, the phenomenon of delayed fertilization in Castanea Miller species (Fagaceae), which are the economically important species of Fagaceae and widely distributed or cultured in many countries of the world, has been consistently neglected, raising questions regarding what the delayed fertilization process is and why fertilization is delayed. To answer these questions, we systematically investigated the micro- and megasporogenesis in addition to male and female gametogenesis in Castanea henryi (Castanea Miller species). Our results show that the ovules primordia are immature at the time of pollination and require 6 weeks to become fully developed. During this 6-week period, 32.30 % of ovules abort because of the inability to form an embryo sac (ES). Approximately 15.79 % of ovules abort because of abnormal development of ES. From 7 to 8 weeks after pollination in which double fertilization occurs, most mature ovules are also aborted because of cell degeneration in gametophytes. Only one ovule can develop into a ripe seed. Thus, the delayed fertilization in Castanea henryi may be necessary to increase the time for mate choice and selective fertilization. A certain number of ovule abortions may be the result of delayed fertilization to maximize reproductive success.

Removal of competitive native species combined with tree planting can accelerate the initial afforestation process: an experiment in an old field in Japan invaded by dwarf bamboo and kudzu

Restoring natural forests after field abandonment is a land management objective that fosters the recovery of forest biodiversity. We performed seeding and transplanting of native tree species 40 years after the abandonment of an arable field that became dominated by a dwarf bamboo (Pleioblastus chino (Franch. et Sav.) Makino) and by kudzu (Pueraria lobata (Willd.) Ohwi). By permutation tests, the removal of competing vegetation (gap creation) significantly increased the survival of three seeded species of Fagaceae and of eight transplanted species. In contrast, intact vegetation prevented most individuals of all species from surviving for 1 year after planting. The lack of natural recruitment of Fagaceae in the nonseeded subplots indicated that seed limitation was a cause of the slow afforestation. Although litter accumulation in gaps at the time of seeding slightly increased survival for late-germinating Quercus myrsinifolia Blume and Castanopsis sieboldii (Makino) Hatus. ex T. Yamaz. et Mashiba, the effect was not consistent among plots and was not statistically significant. Our results suggest that for successful afforestation using native trees in abandoned fields, it will be necessary to remove competitive native species to avoid severe limitations on microsite availability and that simultaneous tree establishment by seeding or transplanting should be implemented to accelerate the establishment of native tree species.

A new bacterial disease observed onQuercus myrsinifolia

This is the first report of a new bacterial disease occurring on Quercus myrsinifolia in the nurseries of the Kyushu district in Japan. The main symptoms are shoot and twig blight, which begins with black necrotic lesions. In addition, unclear blackish discolorations, bacterial ooze and water-soaked lesions were observed as early symptoms, and spindle-shaped cankers and stem cankers with irregular surface were observed as secondary symptoms. The blight symptoms observed on the current-year shoots were first observed during the rainy season and continued until autumn (June–October). In summer, the symptoms were pronounced. A yellowish bacterium was consistently isolated from the affected shoots of Q. myrsinifolia, and on inoculation into healthy trees, it caused the same symptoms, which were more severe after wound inoculation than after non-wound inoculation. Wound inoculation also caused the disease symptoms on Quercus spp., Fagus crenata and Lithocarpus glaber, but not on several other species of Fagaceae. The causal bacterium was identified as Xanthomonas arboricola based on its morphological, cultural and biochemical characteristics and genetic sequence analysis of 16S rDNA, 16S-23S spacer regions and gyrB. To our knowledge, there are no previous records of xanthomonads causing shoot blight on fagaceous plants like Q. myrsinifolia. Therefore, we postulate that the shoot blight of Q. myrsinifolia is a new bacterial disease. We propose the name of the disease to be ‘bacterial shoot blight’ based on its main symptoms.

Molecular organization of the 25S-18S rDNA IGS of Fagus sylvatica and Quercus suber: a comparative analysis.

The 35S ribosomal DNA (rDNA) units, repeated in tandem at one or more chromosomal loci, are separated by an intergenic spacer (IGS) containing functional elements involved in the regulation of transcription of downstream rRNA genes. In the present work, we have compared the IGS molecular organizations in two divergent species of Fagaceae, Fagus sylvatica and Quercus suber, aiming to comprehend the evolution of the IGS sequences within the family. Self- and cross-hybridization FISH was done on representative species of the Fagaceae. The IGS length variability and the methylation level of 18 and 25S rRNA genes were assessed in representatives of three genera of this family: Fagus, Quercus and Castanea. The intergenic spacers in Beech and Cork Oak showed similar overall organizations comprising putative functional elements needed for rRNA gene activity and containing a non-transcribed spacer (NTS), a promoter region, and a 5′-external transcribed spacer. In the NTS: the sub-repeats structure in Beech is more organized than in Cork Oak, sharing some short motifs which results in the lowest sequence similarity of the entire IGS; the AT-rich region differed in both spacers by a GC-rich block inserted in Cork Oak. The 5′-ETS is the region with the higher similarity, having nonetheless different lengths. FISH with the NTS-5′-ETS revealed fainter signals in cross-hybridization in agreement with the divergence between genera. The diversity of IGS lengths revealed variants from ∼2 kb in Fagus, and Quercus up to 5.3 kb in Castanea, and a lack of correlation between the number of variants and the number of rDNA loci in several species. Methylation of 25S Bam HI site was confirmed in all species and detected for the first time in the 18S of Q. suber and Q. faginea. These results provide important clues for the evolutionary trends of the rDNA 25S-18S IGS in the Fagaceae family.

Genetic diversity assessment and estimation of phylogenetic relationships among 26 Fagaceae species using ISSRs

The family Fagaceae includes several species and presents huge genetic variability. In the last two decades, several genetic studies about phylogenetics and genetic diversity of Fagaceae have emerged. ISSR markers were used to evaluate the genetic diversity of 26 species of Fagaceae belonging to the genera Castanea, Fagus and Quercus. Among several primers tested, 17 were selected for the evaluation of diversity and estimation of genetic relationships. A total of 371 ISSR markers were produced and each primer revealed high polymorphism. Specific ISSR markers for the Quercus infrageneric groups were amplified. ISSRs proved to be a reliable tool for the discrimination of the analyzed species per genus, infrageneric group and/or ecological origin.

제주도 자생 참나무과 식물의 대기 중 CO2흡수 능력의 비교분석

The rate of photosynthesis (A) of leaves from 10 plant species (6 evergreen and 4 deciduous) of the family Fagaceae was measured using a portable photosynthesis analyzer, to examine which species take up <TEX>$CO_2$</TEX> most efficiently. Of the evergreen species, the photosynthetic rate of Castanopsis cuspidata var. sieboldii was highest, and remained above 82.1~106.4 <TEX>${\mu}mol\;kg^{-1}s^{-1}$</TEX> from July to November. Of the deciduous species, the photosynthetic rate of Quercus acutissima was higher than that of the other three species, and remained high at 83.5~116.6 <TEX>${\mu}mol\;kg^{-1}s^{-1}$</TEX> from September to November. The photosynthetic rate of the 10 species was positively correlated with stomatal conductance (gs) and transpiration rate (E). However, there was no correlation between photosynthetic rate and intercellular <TEX>$CO_2$</TEX> concentration (<TEX>$C_i$</TEX>), although there was a positive correlation just in three species (Q. gilva, Q. acutissima and Q. glauca). These results suggest that the <TEX>$CO_2$</TEX> fixation capacity of C. cuspidata var. sieboldii, an evergreen species, and Q. acutissima, a deciduous species, is significantly higher than that of the other species examined, and that photosynthesis is regulated by both stomatal conductance and transpiration. Therefore, C. cuspidata var. sieboldii and Q. acutissima may be valuable for the evaluation of carbon uptake in urban green spaces as well as in afforested areas.

A sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genomic libraries

Genomic resources have recently been developed for a number of species of Fagaceae, with the purpose of identifying the genetic factors underlying the adaptation of these long-lived, biologically predominant, commercially and ecologically important species to their environment. The sequencing of genomes of the size of the oak genome (740 Mb/C) is now becoming both possible and affordable due to breakthroughs in sequencing technology. However, an understanding of the composition and structure of the oak genome is required before launching a sequencing initiative. We constructed random (Rd) and hypomethylated (Hp) genomic libraries for pedunculate oak (Quercus robur) and carried out a sample sequencing of 2.33 and 2.36 Mb of shotgun DNA from the Rd and Hp libraries, respectively, to provide a first insight into the repetitive element and gene content of the oak genome. We found striking similarities between Rd sequences and previously analyzed BAC end sequences of pedunculate oak, with a similar percentage of known repeat elements (5.56%), an almost identical simple sequence repeat density (i.e., 29 SSRs per 100 kb), an identical profile of SSR motifs (in descending order of frequency—dinucleotide, pentanucleotide, trinucleotide, tetranucleotide, and hexanucleotide motifs). Conversely, the Hp fraction was, as expected, enriched in nuclear genes (2.44-fold enrichment). This enrichment was associated with a lower frequency of retrotransposons than for Rd sequences. We also identified twice as many SSR motifs in the Rd library as in the Hp library. This work provides useful information before opening a new chapter in oak genome sequencing.