Presented here is a genome sequence of an individual human. It was produced from ∼32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.

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The Diploid Genome Sequence of an Individual Human

Polyploidy is widely acknowledged as a major mechanism of adaptation and speciation in plants. The stages in polyploid evolution include frequent fertility bottlenecks and infrequent events such as gametic nonreduction and interspecific hybridization, yet little is known about how these and other factors influence overall rates of polyploid formation. Here we review the literature regarding polyploid origins, and quantify parameter values for each of the steps involved in the principal pathways. In contrast to the common claim that triploids are sterile, our results indicate that the triploid bridge pathway can contribute significantly to autopolyploid formation regardless of the mating system, and to allopolyploid formation in outcrossing taxa. We estimate that the total rate of autotetraploid formation is of the same order as the genic mutation rate (10 i5 ), and that a high frequency of interspecific hybridization (0.2% for selfing taxa, 2.7% for outcrossing taxa) is required for the rate of tetraploid formation via allopolyploidy to equal that by autopolyploidy. We conclude that the rate of autopolyploid formation may often be higher than the rate of allopolyploid formation. Further progress toward understanding polyploid origins requires studies in natural populations that quantify: (a) the frequency of unreduced gametes, (b) the effectiveness of triploid bridge pathways, and (c) the rates of interspecific hybridization.

/pdf/pathways-mechanisms-and-rates-of-polyploid-formation-in-45lhl9s528.pdf

Pathways, mechanisms, and rates of polyploid formation in flowering plants

Chromosome aberrations, in particular translocations and their corresponding gene fusions, have an important role in the initial steps of tumorigenesis; at present, 358 gene fusions involving 337 different genes have been identified. An increasing number of gene fusions are being recognized as important diagnostic and prognostic parameters in malignant haematological disorders and childhood sarcomas. The biological and clinical impact of gene fusions in the more common solid tumour types has been less appreciated. However, an analysis of available data shows that gene fusions occur in all malignancies, and that they account for 20% of human cancer morbidity. With the advent of new and powerful investigative tools that enable the detection of cytogenetically cryptic rearrangements, this proportion is likely to increase substantially.

The impact of translocations and gene fusions on cancer causation

The Allium test is suggested as a standard in environmental monitoring, e. g. as a part of a test battery. Background, the method including suggested parameters for standard use, results from various application areas and comparisons with a number of other test systems are presented. The Allium test is a short-term test with many advantages: low cost, ease to handle, good chromosome conditions for the study of chromosome damage or disturbance of cell division including the evaluation of risks of aneuploidy. The ability of the root cells to activate promutagens (the MFO-system) further widens the application areas of the Allium test. The use of series of onions for each concentration of the test chemical allows statistical considerations, and from growth curves Effect-Concentration values are obtained. The Allium test is, lastly, a sensitive test showing good correlation to other test systems. Thus, positive results in the Allium test should be considered as a warning and also an indication that the tested chemical may be a risk to human health and to our environment.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.1985.tb00471.x

The Allium test as a standard in environmental monitoring

▪ Abstract Here we review the biology of early generation neopolyploids and discuss the profound changes that accompany their formation. Newly formed auto- and allopolyploids exhibit considerable meiotic complexity, including multivalent pairing, multisomic inheritance, and the production of unbalanced gametes. The cytogenetic behavior of allopolyploids and autopolyploids differ statistically, but are more similar than commonly believed. The progeny of neopolyploids include a high frequency of aneuploids, pseudoeuploids and homeologue-recombinant genotypes that may contribute to the phenotypic variability observed in early generation polyploids. We find no evidence to support the traditional view that autopolyploids possess lower fertility than allopolyploids, casting doubt on the paradigm that allopolyploids should be more frequent due to their inherent fertility. The fertility of early generation polyploids increases rapidly, owing largely to selection against meiotic configurations that generate unbala...

/pdf/neopolyploidy-in-flowering-plants-o3qdtfazt6.pdf

Neopolyploidy in flowering plants

N the inorphologic identification of chromosomes, the location of the I centromere is the most useful landmark, and one which is characterized by great constancy. It would seem that not much could be added to the definitions by E. B. WILSON (1928) of the locations on the chromosome of the centrornere or, in the terminology of that time, the spindle attachment: “Attachment of the chromosome to the spindle is commonly limited to a small area, and is of two general types, namely: (1) terminnl or telomitic and (2) non-ferminal or atelomitic, being in the former case at one end, and in the latter at some other point or points. Non-terminal attachment may be at the middle point (median) or at an intermediate point (submedian, sub-terminal). All gradations exist between these various cases;” (I.c., p. 130-131). In the acconipanying picture (l.c., Fig. 56, p. 132), here reprinted as Fig. l., the four locations of median, submedian, subterminal and terminal are represented, and, in addition, “lateral”, which corresponds to the modern term “diffuse centromere”. Nevertheless, at the present time, with the immense increase in research activity in mammalian cytology, the terminology of the centromeric position has become burdened by much obscurity and confusion. One cause of confusion is that different authors, and even the same author on different occasions, have used the terms median, submedian etc. with great amplitude, and it is often difficult to know in a specific case what each term signifies. Another cause of confusion is that a set of terms for chromosomes with specific centromeric positions, such as metacentric, acrocentric, telocentric, have come into wide usage without being clearly defined in relation to the positional terms median, submedian, subterminal and terminal. During the spring of 1963 the present writers exchanged epistolary

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.1964.tb01953.x

Nomenclature for centromeric position on chromosomes

While staying last summer at the Sloan-Kettering Institute, New York, one of us tried out some modifications of Hsu’s technique (1952) on various human tissue cultures carried in serial in vitro cultivation at that institute. The results were promising inasmuch as some fairly satisfactory chromosome analyses were obtained in cultures both of tissues of normal origin and of tumours (Levan, 1956).

https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1601-5223.1956.tb03010.x

The chromosome number of man

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.1938.tb03221.x

Albert Levan

Papers

Nomenclature for centromeric position on chromosomes

The chromosome number of man

The effect of colchicine on root mitoses in allium

Cytological phenomena connected with the root swelling caused by growth substances

Induction of chromosome fragmentation by phenols