The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Mark D Burow - One of the best experts on this subject based on the ideXlab platform.
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transcriptome sequencing of diverse peanut arachis wild Species and the Cultivated Species reveals a wealth of untapped genetic variability
G3: Genes Genomes Genetics, 2016Co-Authors: Ratan Chopra, Gloria Burow, C E Simpson, Jennifer Chagoya, Joann Mudge, Mark D BurowAbstract:To test the hypothesis that the Cultivated peanut Species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild Species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 Cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and Cultivated tetraploids by subSpecies. Cluster analysis of variants indicated that sequences of B genome Species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome Species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild Species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the Cultivated Species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.
Bruce J Paster - One of the best experts on this subject based on the ideXlab platform.
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diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients
Journal of Clinical Microbiology, 2003Co-Authors: C E Kazor, P M Mitchell, Lauren N Stokes, W J Loesche, Floyd E Dewhirst, Bruce J PasterAbstract:The primary purpose of the present study was to compare the microbial profiles of the tongue dorsa of healthy subjects and subjects with halitosis by using culture-independent molecular methods. Our overall goal was to determine the bacterial diversity on the surface of the tongue dorsum as part of our ongoing efforts to identify all cultivable and not-yet-Cultivated Species of the oral cavity. Tongue dorsum scrapings were analyzed from healthy subjects with no complaints of halitosis and subjects with halitosis, defined as an organoleptic score of 2 or more and volatile sulfur compound levels greater than 200 ppb. 16S rRNA genes from DNA isolated from tongue dorsum scrapings were amplified by PCR with universally conserved bacterial primers and cloned into Escherichia coli. Typically, 50 to 100 clones were analyzed from each subject. Fifty-one strains isolated from the tongue dorsa of healthy subjects were also analyzed. Partial sequences of approximately 500 bases of cloned inserts from the 16S rRNA genes of isolates were compared with sequences of known Species or phylotypes to determine Species identity or closest relatives. Nearly complete sequences of about 1,500 bases were obtained for potentially novel Species or phylotypes. In an analysis of approximately 750 clones, 92 different bacterial Species were identified. About half of the clones were identified as phylotypes, of which 29 were novel to the tongue microbiota. Fifty-one of the 92 Species or phylotypes were detected in more than one subject. Those Species most associated with healthy subjects were Streptococcus salivarius, Rothia mucilaginosa, and an uncharacterized Species of Eubacterium (strain FTB41). Streptococcus salivarius was the predominant Species in healthy subjects, as it represented 12 to 40% of the total clones analyzed from each healthy subject. Overall, the predominant microbiota on the tongue dorsa of healthy subjects was different from that on the tongue dorsa of subjects with halitosis. Those Species most associated with halitosis were Atopobium parvulum, a phylotype (clone BS095) of Dialister, Eubacterium sulci, a phylotype (clone DR034) of the unCultivated phylum TM7, Solobacterium moorei, and a phylotype (clone BW009) of Streptococcus. On the basis of our ongoing efforts to obtain full 16S rRNA sequences for all cultivable and not-yet-Cultivated Species that colonize the oral cavity, there are now over 600 Species.
David M Spooner - One of the best experts on this subject based on the ideXlab platform.
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taxonomy of Cultivated potatoes solanum section petota solanaceae
Botanical Journal of the Linnean Society, 2011Co-Authors: Anna Ovchinnikova, Ekaterina Krylova, Tatjana Gavrilenko, Tamara Smekalova, Mikhail Zhuk, Sandra Knapp, David M SpoonerAbstract:Solanum tuberosum, the Cultivated potato of world commerce, is a primary food crop worldwide. Wild and Cultivated potatoes form the germplasm base for international breeding efforts to improve potato in the face of a variety of disease, environmental and agronomic constraints. A series of national and international genebanks collect, characterize and distribute germplasm to stimulate and aid potato improvement. A knowledge of potato taxonomy and evolution guides collecting efforts, genebank operations and breeding. Past taxonomic treatments of wild and Cultivated potato have differed tremendously among authors with regard to both the number of Species recognized and the hypotheses of their interrelationships. In total, there are 494 epithets for wild and 626 epithets for Cultivated taxa, including names not validly published. Recent classifications, however, recognize only about 100 wild Species and four Cultivated Species. This paper compiles, for the first time, the epithets associated with all taxa of Cultivated potato (many of which have appeared only in the Russian literature), places them in synonymy and provides lectotype designations for all names validly published where possible. We also summarize the history of differing taxonomic concepts in Cultivated potato, and provide keys and descriptions for the four Cultivated Species. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165, 107-155.
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extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: David M Spooner, Jorge Nunez, Guillermo Trujillo, Maria Del Rosario Herrera, Frank Guzman, Marc GhislainAbstract:Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean Species, or of Cultivar Groups within the single Species Solanum tuberosum. We provide one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all Cultivated Species (or Cultivar Groups) and 8 closely related wild Species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: (i) putative diploids, (ii) putative tetraploids, and (iii) the hybrid Cultivated Species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtilobum (pentaploid). However, there are many exceptions to grouping by ploidy. Strong statistical support occurs only for S. ajanhuiri, S. juzepczukii, and S. curtilobum. In combination with recent morphological analyses and an examination of the identification history of these collections, we support the reclassification of the Cultivated potatoes into four Species: (i) S. tuberosum, with two Cultivar Groups (Andigenum Group of upland Andean genotypes containing diploids, triploids, and tetraploids, and the Chilotanum Group of lowland tetraploid Chilean landraces); (ii) S. ajanhuiri (diploid); (iii) S. juzepczukii (triploid); and (iv) S. curtilobum (pentaploid). For other classifications, consistent and stable identifications are impossible, and their classification as Species is artificial and only maintains the confusion of users of the gene banks and literature.
Sandra Knapp - One of the best experts on this subject based on the ideXlab platform.
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a phylogenetic framework for evolutionary study of the nightshades solanaceae a dated 1000 tip tree
BMC Evolutionary Biology, 2013Co-Authors: Lynn Bohs, Tiina Sarkinen, Richard G Olmstead, Sandra KnappAbstract:Background The Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular Cultivated Species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. Here we investigate molecular divergence times for Solanaceae using a densely-sampled Species-level phylogeny. We also review the fossil record of the family to derive robust calibration points, and estimate a chronogram using an uncorrelated relaxed molecular clock.
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taxonomy of Cultivated potatoes solanum section petota solanaceae
Botanical Journal of the Linnean Society, 2011Co-Authors: Anna Ovchinnikova, Ekaterina Krylova, Tatjana Gavrilenko, Tamara Smekalova, Mikhail Zhuk, Sandra Knapp, David M SpoonerAbstract:Solanum tuberosum, the Cultivated potato of world commerce, is a primary food crop worldwide. Wild and Cultivated potatoes form the germplasm base for international breeding efforts to improve potato in the face of a variety of disease, environmental and agronomic constraints. A series of national and international genebanks collect, characterize and distribute germplasm to stimulate and aid potato improvement. A knowledge of potato taxonomy and evolution guides collecting efforts, genebank operations and breeding. Past taxonomic treatments of wild and Cultivated potato have differed tremendously among authors with regard to both the number of Species recognized and the hypotheses of their interrelationships. In total, there are 494 epithets for wild and 626 epithets for Cultivated taxa, including names not validly published. Recent classifications, however, recognize only about 100 wild Species and four Cultivated Species. This paper compiles, for the first time, the epithets associated with all taxa of Cultivated potato (many of which have appeared only in the Russian literature), places them in synonymy and provides lectotype designations for all names validly published where possible. We also summarize the history of differing taxonomic concepts in Cultivated potato, and provide keys and descriptions for the four Cultivated Species. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165, 107-155.
Jennifer Chagoya - One of the best experts on this subject based on the ideXlab platform.
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transcriptome sequencing of diverse peanut arachis wild Species and the Cultivated Species reveals a wealth of untapped genetic variability
G3: Genes Genomes Genetics, 2016Co-Authors: Ratan Chopra, Gloria Burow, C E Simpson, Jennifer Chagoya, Joann Mudge, Mark D BurowAbstract:To test the hypothesis that the Cultivated peanut Species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild Species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 Cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and Cultivated tetraploids by subSpecies. Cluster analysis of variants indicated that sequences of B genome Species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome Species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild Species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the Cultivated Species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.