Genomic and Epigenetic Foundations of Neocentromere Formation

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Evon M. DeBose-Scarlett ◽  
Beth A. Sullivan
Keyword(s):  
Genome Instability ◽  
Genome Project ◽  
Model Organisms ◽  
Annual Review ◽  
Publication Date ◽  
Open Chromatin ◽  
Developmental Defects ◽  
Active Transcription ◽  
Genomic Locations ◽  
The Human Genome Project

Centromeres are essential to genome inheritance, serving as the site of kinetochore assembly and coordinating chromosome segregation during cell division. Abnormal centromere function is associated with birth defects, infertility, and cancer. Normally, centromeres are assembled and maintained at the same chromosomal location. However, ectopic centromeres form spontaneously at new genomic locations and contribute to genome instability and developmental defects as well as to acquired and congenital human disease. Studies in model organisms have suggested that certain regions of the genome, including pericentromeres, heterochromatin, and regions of open chromatin or active transcription, support neocentromere activation. However, there is no universal mechanism that explains neocentromere formation. This review focuses on recent technological and intellectual advances in neocentromere research and proposes future areas of study. Understanding neocentromere biology will provide a better perspective on chromosome and genome organization and functional context for information generated from the Human Genome Project, ENCODE, and other large genomic consortia. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

What Do We Know About the Genetic Architecture of Psychopathology?

2022 ◽  
Vol 18 (1) ◽  
Author(s):  
Evan J. Giangrande ◽  
Ramona S. Weber ◽  
Eric Turkheimer
Keyword(s):  
Twin Study ◽  
Human Genome Project ◽  
Genetic Architecture ◽  
Genome Project ◽  
Reasonable Doubt ◽  
Annual Review ◽  
Publication Date ◽  
Biological Insight ◽  
The Human Genome Project ◽  
Paradigm Shifting

In the second half of the twentieth century, twin and family studies established beyond a reasonable doubt that all forms of psychopathology are substantially heritable and highly polygenic. These conclusions were simultaneously an important theoretical advance and a difficult methodological obstacle, as it became clear that heritability is universal and undifferentiated across forms of psychopathology, and the radical polygenicity of genetic effects limits the biological insight provided by genetically informed studies at the phenotypic level. The paradigm-shifting revolution brought on by the Human Genome Project has recapitulated the great methodological promise and the profound theoretical difficulties of the twin study era. We review these issues using the rubric of genetic architecture, which we define as a search for specific genetic insight that adds to the general conclusion that psychopathology is heritable and polygenic. Although significant problems remain, we see many promising avenues for progress. Expected final online publication date for the Annual Review of Clinical Psychology, Volume 18 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Growth and Division of the Peptidoglycan Matrix

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Patricia D.A. Rohs ◽  
Thomas G. Bernhardt
Keyword(s):  
Cell Wall ◽  
Bacterial Infections ◽  
Model Organisms ◽  
Annual Review ◽  
Publication Date ◽  
Drug Resistant ◽  
Peptidoglycan Cell Wall ◽  
Integral Role ◽  
Osmotic Lysis ◽  
Peptidoglycan Layer

Most bacteria are surrounded by a peptidoglycan cell wall that defines their shape and protects them from osmotic lysis. The expansion and division of this structure therefore plays an integral role in bacterial growth and division. Additionally, the biogenesis of the peptidoglycan layer is the target of many of our most effective antibiotics. Thus, a better understanding of how the cell wall is built will enable the development of new therapies to combat the rise of drug-resistant bacterial infections. This review covers recent advances in defining the mechanisms involved in assembling the peptidoglycan layer with an emphasis on discoveries related to the function and regulation of the cell elongation and division machineries in the model organisms Escherichia coli and Bacillus subtilis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Overview: A System for Tracking and Managing the Results from Sequence Comparison Programs

1999 ◽  
Author(s):  
David P. Yee ◽  
Tim Hunkapiller
Keyword(s):  
Human Genome ◽  
Human Genome Project ◽  
High Speed ◽  
Genomic Sequence ◽  
Query Languages ◽  
Genome Project ◽  
Database Management System ◽  
Model Organisms ◽  
Sequence Databases ◽  
The Human Genome Project

The Human Genome Project was launched in the early 1990s to map, sequence, and study the function of genomes derived from humans and a number of model organisms such as mouse, rat, fruit fly, worm, yeast, and Escherichia coli. This ambitious project was made possible by advances in high-speed DNA sequencing technology (Hunkapiller et al., 1991). To date, the Human Genome Project and other large-scale sequencing projects have been enormously successful. The complete genomes of several microbes (such as Hemophilus influenzae Rd, Mycoplasma genitalium, and Methanococcus jannaschii) have been completely sequenced. The genome of bacteriophage T4 is complete, and the 4.6-megabase sequence of E. coli and the 13-megabase genome of Saccharomyces cerevisiae have just recently also been completed. There are 71 megabases of the nematode Caenorhabditis elegans available. Six megabases of mouse and 60 megabases of human genomic sequence have been finished, which represent 0.2% and 2% of their respective genomes. Finally, more than 1 million expressed sequence tags derived from human and mouse complementary DNA expression libraries are publicly available. These public data, in addition to private and proprietary DNA sequence databases, represent an enormous information-processing challenge and data-mining opportunity. The need for common interfaces and query languages to access heterogeneous sequence databases is well documented, and several good systems are well underway to provide those interfaces (Woodsmall and Benson, 1993; Marr, 1996). Our own work on database and program interoperability in this domain and in computational chemistry (Gushing, 1995) has shown, however, that providing the interface is but the first step toward making these databases fully useful to the researcher. (Here, the term “database” means a collection of data in electronic form, which may not necessarily be physically deposited in a database management system [DBMS]. A scientist’s database could thus be a collection of flat files, where the term “database” means “data stored in a DBMS” is clear from the context.) Deciphering the genomes of sequenced organisms falls into the realm of analysis; there is now plenty of sequence data. The most common form of sequence analysis involves the identification of homologous relationships among similar sequences.

Advances in the Evolution and Ecology of 13- and 17-Year Periodical Cicadas

2021 ◽  
Vol 67 (1) ◽  
Author(s):  
Chris Simon ◽  
John R. Cooley ◽  
Richard Karban ◽  
Teiji Sota
Keyword(s):  
Character Displacement ◽  
Prime Numbers ◽  
Life Cycles ◽  
Model Organisms ◽  
Annual Review ◽  
Publication Date ◽  
Reproductive Character Displacement ◽  
Temporal Isolation ◽  
Periodical Cicadas ◽  
Major Review

Apart from model organisms, 13- and 17-year periodical cicadas (Hemiptera: Cicadidae: Magicicada) are among the most studied insects in evolution and ecology. They are attractive subjects because they predictably emerge in large numbers; have a complex biogeography shaped by both spatial and temporal isolation; and include three largely sympatric, parallel species groups that are, in a sense, evolutionary replicates. Magicicada are also relatively easy to capture and manipulate, and their spectacular, synchronized mass emergences facilitate outreach and citizen science opportunities. Since the last major review, studies of Magicicada have revealed insights into reproductive character displacement and the nature of species boundaries, provided additional examples of allochronic speciation, found evidence for repeated and parallel (but noncontemporaneous) evolution of 13- and 17-year life cycles, quantified the amount and direction of gene flow through time, revealed phylogeographic patterning resulting from paleoclimate change, studied the timing of juvenile development, and created hypotheses for the evolution of life-cycle control and the future effects of climate change on Magicicada life cycles. New ecological studies have supported and questioned the role of prime numbers in Magicicada ecology and evolution, found bidirectional shifts in population size over generations, quantified the contribution of Magicicada to nutrient flow in forest ecosystems, and examined behavioral and biochemical interactions between Magicicada and their fungal parasites and bacterial endosymbionts. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Green Algal Models for Multicellularity

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
James Umen ◽  
Matthew D. Herron
Keyword(s):  
Single Cells ◽  
Model Organisms ◽  
Annual Review ◽  
Publication Date ◽  
Freshwater Algae ◽  
Green Algal ◽  
Photosynthetic Eukaryotes ◽  
Volvocine Algae ◽  
Repeated Evolution ◽  
Life On Earth

The repeated evolution of multicellularity across the tree of life has profoundly affected the ecology and evolution of nearly all life on Earth. Many of these origins were in different groups of photosynthetic eukaryotes, or algae. Here, we review the evolution and genetics of multicellularity in several groups of green algae, which include the closest relatives of land plants. These include millimeter-scale, motile spheroids of up to 50,000 cells in the volvocine algae; decimeter-scale seaweeds in the genus Ulva (sea lettuce); and very plantlike, meter-scale freshwater algae in the genus Chara (stoneworts). We also describe algae in the genus Caulerpa, which are giant, multinucleate, morphologically complex single cells. In each case, we review the life cycle, phylogeny, and genetics of traits relevant to the evolution of multicellularity, and genetic and genomic resources available for the group in question. Finally, we suggest routes toward developing these groups as model organisms for the evolution of multicellularity. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

What Have We Learned from the First 500 Avian Genomes?

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Gustavo A. Bravo ◽  
C. Jonathan Schmitt ◽  
Scott V. Edwards
Keyword(s):  
Population Genomics ◽  
Sequence Data ◽  
Genome Project ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Bird Diversity ◽  
Annual Review ◽  
Publication Date ◽  
Genomic Changes ◽  
Rare Genomic Changes

The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Revelations About Aging and Disease from Unconventional Vertebrate Model Organisms

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Yang Zhao ◽  
Andrei Seluanov ◽  
Vera Gorbunova
Keyword(s):  
Risk Factor ◽  
Animal Species ◽  
Model Organisms ◽  
Annual Review ◽  
Publication Date ◽  
Vertebrate Species ◽  
Associated Diseases ◽  
Vertebrate Model ◽  
Underlying Mechanisms ◽  
Excellent Resource

Aging is a major risk factor for multiple diseases. Understanding the underlying mechanisms of aging would help to delay and prevent age-associated diseases. Short-lived model organisms have been extensively used to study the mechanisms of aging. However, these short-lived species may be missing the longevity mechanisms that are needed to extend the lifespan of an already long-lived species such as humans. Unconventional long-lived animal species are an excellent resource to uncover novel mechanisms of longevity and disease resistance. Here, we review mechanisms that evolved in nonmodel vertebrate species to counteract age-associated diseases. Some antiaging mechanisms are conserved across species; however, various nonmodel species also evolved unique mechanisms to delay aging and prevent disease. This variety of antiaging mechanisms has evolved due to the remarkably diverse habitats and behaviors of these species. We propose that exploring a wider range of unconventional vertebrates will provide important resources to study antiaging mechanisms that are potentially applicable to humans. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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