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"Jenkins, Jerry"
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Sedges of the Northern Forest : a photographic guide
\"A visual reference for identification of the approximately 236 sedges of the Northern Forest Region, with quick guides, systematic sections, annotations, and notes. Accompanying folding charts for field use sold separately\"-- Provided by publisher.
Book
A willow sex chromosome reveals convergent evolution of complex palindromic repeats
Background
Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination.
Results
Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub
Salix purpurea
. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus
Populus
, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes.
Conclusion
The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.
Journal Article
Verbal judo : the gentle art of persuasion
\"Verbal Judo is the classic guide to the martial art of the mind and mouth that can help you defuse confrontations and generate cooperation, whether you're talking to a boss, a spouse, or even a teenager. For more than a generation, Dr. George J. Thompson's essential handbook has taught people how to communicate more confidently and persuasively in any situation. Verbal Judo shows you how to listen and speak more effectively, engage others through empathy (the most powerful word in the English language), avoid the most common conversational disasters, and use proven strategies to successfully express your point of view--and take the lead in most disputes. This updated edition includes a new foreword and a chapter featuring Dr. Thompson's five universal truths of 'human interaction'\" --P. 4 of cover.
Book
The barley pan-genome reveals the hidden legacy of mutation breeding
Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’
1
). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (
Hordeum vulgare
L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions
2
. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement
Journal Article
The genome sequence of segmental allotetraploid peanut Arachis hypogaea
Like many other crops, the cultivated peanut (
Arachis hypogaea
L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart
A. monticola
. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid
A. hypogaea
over other diploid
Arachis
species cultivated by humans.
The genome sequence of segmental allotetraploid peanut suggests that diversity generated by genetic deletions and homeologous recombination helped to favor the domestication of
Arachis hypogaea
over its diploid relatives.
Journal Article
Billions of years, amazing changes : the story of evolution
Traces the history of man's discoveries about evolution, covering both the mechanisms of evolution and examples of natural selection-- source other than Library of Congress.
Book
Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade‐off with American chestnut ancestry implies resistance is polygenic
American chestnut was once a foundation species of eastern North American forests, but was rendered functionally extinct in the early 20th century by an exotic fungal blight (Cryphonectria parasitica). Over the past 30 years, the American Chestnut Foundation (TACF) has pursued backcross breeding to generate hybrids that combine the timber‐type form of American chestnut with the blight resistance of Chinese chestnut based on a hypothesis of major gene resistance. To accelerate selection within two backcross populations that descended from two Chinese chestnuts, we developed genomic prediction models for five presence/absence blight phenotypes of 1,230 BC3F2 selection candidates and average canker severity of their BC3F3 progeny. We also genotyped pure Chinese and American chestnut reference panels to estimate the proportion of BC3F2 genomes inherited from parent species. We found that genomic prediction from a method that assumes an infinitesimal model of inheritance (HBLUP) has similar accuracy to a method that tends to perform well for traits controlled by major genes (Bayes C). Furthermore, the proportion of BC3F2 trees' genomes inherited from American chestnut was negatively correlated with the blight resistance of these trees and their progeny. On average, selected BC3F2 trees inherited 83% of their genome from American chestnut and have blight resistance that is intermediate between F1 hybrids and American chestnut. Results suggest polygenic inheritance of blight resistance. The blight resistance of restoration populations will be enhanced through recurrent selection, by advancing additional sources of resistance through fewer backcross generations, and by potentially by breeding with transgenic blight‐tolerant trees.
Journal Article
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity
Background
The availability of the peach genome sequence has fostered relevant research in peach and related
Prunus
species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches.
Results
Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%.
Conclusions
The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related
Prunus
species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.
Journal Article
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Stephen Wright, Detlef Weigel and colleagues report the whole-genome sequence of
Capsella rubella
, a highly selfing crucifer found throughout much of southern and western Europe. They compare mixed-stage flower bud transcriptomes from
C. rubella
and
C. grandiflora
, finding a shift in expression of genes associated with flowering phenotypes and providing insights into the transition to selfing.
The shift from outcrossing to selfing is common in flowering plants
1
,
2
, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by
Capsella rubella
, which became self compatible <200,000 years ago. We report a
C. rubella
reference genome sequence and compare RNA expression and polymorphism patterns between
C. rubella
and its outcrossing progenitor
Capsella grandiflora
. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in
Arabidopsis
, in which self fertilization evolved about 1 million years ago. Comparisons of the two
Capsella
species showed evidence of rapid genome-wide relaxation of purifying selection in
C. rubella
without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
Journal Article