Cultivar Identification and Genetic Relatedness Among 25 Black Walnut (Juglans Nigra) Clones Based on Microsatellite Markers

A set of eight microsatellite markers was used to genotype 25 black walnut (Juglans nigra L.) clones within the Purdue University germplasm repository. The identities of 212 ramets were verified using the same eight microsatellite markers. Some trees were mislabeled and corrected as to clone using analysis of microsatellite markers. A genetic dendrogram was constructed to show the degree of genetic relatedness between clones. Two additional dendrograms, one based on crown architecture traits and the other on tree size and form traits, were also built and compared with the genetic dendrogram. The genetic dendrogram showed that these eight molecular markers had the ability to distinguish genetically related clones from less related ones. Crown architecture traits and tree size and form traits were able to group genetically related clones together, but less accurately than the genetic matrix

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut [version 2; referees: 3 approved]

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software

Black Walnut

Black walnut (Juglans nigra L.), also known as eastern black walnut or American walnut, is a fine hardwood species in the family Juglandaceae, section Rhysocaryon (Manning 1978). In general, J. nigra will not cross with species in the sections Cardiocaryon or Trachycaryonv, but J. nigra will cross with J. ailantifolia (Cardiocaryon) (Williams 1990). Juglans nigra will also hybridize to some extent with other Juglans species (Dioscaryon and Rhysocaryon), and one hybrid is recognized: J. nigra × J. regia = J. x intermedia Carr. (USDA-NRCS 2004). Native to the deciduous forests of the eastern United States (USA), from Massachusetts to Florida and west to Minnesota and Texas, and occurring naturally in southern Ontario, Canada, black walnut is seldom found in pure stands, but rather in association with five mixed mesophytic forest cover types: sugar maple, yellow poplar, yellow poplar – white oak – northern red oak, beech – sugar maple, and silver maple – American elm (Williams 1990). Black walnut is a large tree and on good sites may attain a height of 30 to 38 m and diameter of 76 to 120 cm and can exceed 100 years of age (Williams 1990; Dirr 1998; USDA-NRCS 2004). Black walnut is shade intolerant, and control of competing vegetation is especially important in new plantations for the first 3 to 4 years. Black walnut grows best on moist, deep, fertile, well-drained, loamy soils, although it also grows quite well in silty clay loam soils or in good agricultural soils without a fragipan (Williams 1990; Cogliastro et al. 1997). These sites include coves, bottomlands, abandoned agricultural fields, and rich woodlands. Black walnut forms a deep taproot, wide-spreading lateral roots, and has been cultivated since 1686. A toxic chemical ‘juglone’ (5- hydroxy-1, 4-naphthoquinone), naturally occurring in the leaves, buds, bark, nut husks, and roots of black walnut, is a highly selective, cell-permeable, irreversible inhibitor of the parvulin family of peptidylprolyl cis/trans isomerases (PPIases) and functions by covalently modifying sullfhydryl groups in the target enzymes (Henning et al. 1998; Chao et al. 2001). Certain plants, especially tomato, apple, and several conifer species, are adversely affected (allelopathy; foliar yellowing, wilting, and even death) by being grown near the roots of black walnut trees (Goodell 1984; Dana and Lerner 1994). Horses can contract acute laminitis, an inflammation of the foot, when black walnut wood chips or sawdust is used for stall bedding or stables and paddocks are located too close to walnut trees (Galey et al. 1991). Historically, the bark of black walnut was used by several Native Americans, including the Cherokee, Delaware, Iroquois, and Meskwaki, in tea as a cathartic, emetic, or disease remedy agent, and chewed or applied for toothaches, snake bites, and headaches (Moerman 1998, 2003). Caution: the bark should be used cautiously inmedicine because it is poisonous. TheCherokee, Chippewa, and Meskwaki also used the bark to make a dark brown or black dye (Moerman 1998, 2003). The Comanche pulverized the leaves of black walnut for treatment of ringworm, the Cherokee used leaves to make a green dye, and the Delaware used the leaves as an insecticide to dispel fleas (Moerman 1998, 2003). The nut meats were also a food source for Native Americans, and the nuts are still consumed today by people and are an important food source for wildlife

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