The complete sequence of a human genome

In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.

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International Human Genome Sequencing Consortium Publishes Sequence and Analysis of the Human Genome

PsycEXTRA Dataset ◽

10.1037/e634052007-001 ◽

2001 ◽

Keyword(s):

Human Genome ◽

Genome Sequencing ◽

Genome Sequencing Consortium ◽

Human Genome Sequencing ◽

International Human

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Genetic and brain imaging contributions to neuropsychological functioning in preclinical dementia

Journal of the International Neuropsychological Society ◽

10.1017/s1355617702870059 ◽

2002 ◽

Vol 8 (7) ◽

pp. 915-917 ◽

Cited By ~ 4

Author(s):

MARK W. BONDI

Keyword(s):

Human Genome ◽

Cholinesterase Inhibitors ◽

Neuropsychological Functioning ◽

Clinical Manifestations ◽

The Past ◽

Preclinical Phase ◽

Genome Sequencing Consortium ◽

Human Genome Sequencing ◽

Brain Changes ◽

International Human

A veritable explosion of research in neuropsychology has occurred over the past decade in the search for cognitive and brain changes during a so-called “preclinical” phase of dementia that precedes its overt clinical manifestations. Fueling this explosion, in part, has been the revolution in the genetic bases of disease formulated from the international work of decoding the human genome (International Human Genome Sequencing Consortium, 2001; see also Patenaude et al., 2002, for discussion). The discovery of preclinical cognitive, brain, and genetic markers of dementia is helping to push back the point at which diseases can be reliably identified. Very early detection of dementia is extremely important now that a variety of investigational treatments that might prevent or delay disease progression (e.g., amyloid vaccine, anti-oxidants, nonsteroidal anti-inflammatory agents, cholinesterase inhibitors, estrogens, and others in the case of Alzheimer's disease) are on the horizon.

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A reference-quality, fully annotated genome from a Puerto Rican individual

10.1101/2021.06.10.447952 ◽

2021 ◽

Author(s):

Aleksey V Zimin ◽

Alaina Shumate ◽

Ida Shinder ◽

Jakob Heinz ◽

Daniela Puiu ◽

...

Keyword(s):

Puerto Rican ◽

Human Genome ◽

Reference Genome ◽

Individual Genome ◽

Protein Coding ◽

Human Reference Genome ◽

Gene Copies ◽

Reference Quality ◽

Assembly Technology ◽

Individual Human

Until 2019, the human genome was available in only one fully-annotated version, which was the result of 18 years of continuous improvement and revision. Despite dramatic improvements in sequencing technology, no other individual human genome was available as an annotated reference until 2019, when the genome of an Ashkenazi individual was released. In this study, we describe the assembly and annotation of a second individual genome, from a Puerto Rican individual whose DNA was collected as part of the Human Pangenome project. The new genome, called PR1, is the first true reference genome created from an individual of African descent. Due to recent improvements in both sequencing and assembly technology, PR1 is more complete and more contiguous than either the human reference genome (GRCh38) or the Ashkenazi genome. Annotation revealed 42,217 genes (of which 20,168 are protein-coding), including 107 additional gene copies that are present in PR1 and missing from GRCh38. 180 genes have fewer copies in PR1 than in GRCh38, 13 map only partially, and 3 genes (1 protein-coding) from GRCh38 are entirely missing from PR1.

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A reference-quality, fully annotated genome from a Puerto Rican individual

Genetics ◽

10.1093/genetics/iyab227 ◽

2021 ◽

Author(s):

Aleksey V Zimin ◽

Alaina Shumate ◽

Ida Shinder ◽

Jakob Heinz ◽

Daniela Puiu ◽

...

Keyword(s):

Puerto Rican ◽

Human Genome ◽

Continuous Improvement ◽

Reference Genome ◽

Sequencing Technology ◽

Individual Genome ◽

Protein Coding ◽

Gene Copies ◽

Reference Quality ◽

Assembly Technology

Abstract Until 2019, the human genome was available in only one fully-annotated version, GRCh38, which was the result of 18 years of continuous improvement and revision. Despite dramatic improvements in sequencing technology, no other genome was available as an annotated reference until 2019, when the genome of an Ashkenazi individual, Ash1, was released. In this study, we describe the assembly and annotation of a second individual genome, from a Puerto Rican individual whose DNA was collected as part of the Human Pangenome project. The new genome, called PR1, is the first true reference genome created from an individual of African descent. Due to recent improvements in both sequencing and assembly technology, and particularly to the use of the recently completed CHM13 human genome as a guide to assembly, PR1 is more complete and more contiguous than either GRCh38 or Ash1. Annotation revealed 37,755 genes (of which 19,999 are protein-coding), including 12 additional gene copies that are present in PR1 and missing from CHM13. 57 genes have fewer copies in PR1 than in CHM13, 9 map only partially, and 3 genes (all non-coding) from CHM13 are entirely missing from PR1.

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Introduction to Genomics Sequencing

Public Health Genomics and International Wealth Creation - Advances in Human Services and Public Health ◽

10.4018/978-1-4666-8559-8.ch001 ◽

2016 ◽

pp. 1-22

Keyword(s):

Human Genome ◽

Genome Sequencing ◽

The United States ◽

Employment Opportunities ◽

Sequencing Project ◽

The United Kingdom ◽

Genome Sequencing Consortium ◽

Human Genome Sequencing ◽

International Human ◽

International Experts

At the outset, we defined genome, and explored the initiation of the Human Genome Sequencing project (HGSP). A synopsis of the various national and international experts and pioneers who were involved in the sequencing project were identified. This team eventually became the International Human Genome Sequencing Consortium (IHGSC). The nations that collaborated and contributed toward the successful sequencing were basically the United States (U.S.), France, the United Kingdom, Japan, Italy, and China. The accomplishment of the human genome sequencing was completed at ahead of schedule and by March 25, 2003 the project had accomplished all the publicized objectives of the project. The potential career paths and employment opportunities associated with the human genome sequencing were identified.

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The complete mitochondrial genome of the freshwater crab Longpotamon kenliense (Decapoda, Brachyura, Potamidae) with phylogenetic consideration

Crustaceana ◽

10.1163/15685403-bja10085 ◽

2020 ◽

Vol 93 (11-12) ◽

pp. 1277-1293

Author(s):

Yi-Fan Wang ◽

Shu-Xin Xu ◽

Chun-Chao Zhu ◽

Xin-Nan Jia ◽

Xian-Min Zhou ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Divergence Time ◽

Complete Sequence ◽

Divergence Times ◽

Mitochondrial Genomes ◽

Freshwater Crab ◽

Protein Coding ◽

Protein Coding Genes ◽

First Time

Abstract The authors herein report for the first time the complete sequence of the mitochondrial genome of Longpotamon kenliense. The results showed that the mitochondrial genome of L. kenliense is 18,499 bp in length, shares 37 genes and 1 control region with the typical metazoan mitochondrial genome, and has a strong A + T bias (74.48%), i.e., a characteristic of the metazoan mitochondrial genome. In addition, the authors used the 13 protein-coding genes from the mitochondrial genomes of L. kenliense and 67 other species of Brachyura available from the NCBI to estimate divergence times. The divergence time of L. kenliense was 14.39 Ma, which is close to the divergence times of L. xiushuiense and L. yangtsekiense, but later than that of Sinopotamon yaanense. The results indicate that the genera Sinopotamon and Longpotamon are closely related and that the genus Sinopotamon has a longer history, which may have been caused by geological events.

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Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Diversity ◽

10.3390/d13020081 ◽

2021 ◽

Vol 13 (2) ◽

pp. 81

Author(s):

Jakub Sawicki ◽

Katarzyna Krawczyk ◽

Monika Ślipiko ◽

Monika Szczecińska

Keyword(s):

Cryptic Speciation ◽

Editing Event ◽

Protein Coding ◽

Gene Set ◽

Protein Coding Genes ◽

Organellar Genomes ◽

The Family ◽

Leafy Liverwort ◽

Aneura Mirabilis ◽

First Time

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

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Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Genome Biology ◽

10.1186/s13059-021-02369-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Robin-Lee Troskie ◽

Yohaann Jafrani ◽

Tim R. Mercer ◽

Adam D. Ewing ◽

Geoffrey J. Faulkner ◽

...

Keyword(s):

Cultured Cells ◽

Open Reading Frames ◽

Cdna Sequencing ◽

Protein Coding ◽

Dynamic Component ◽

Gene Copies ◽

Long Read ◽

Normal Human ◽

Reading Frames ◽

Transcriptional Landscape

AbstractPseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes expressed in tissue-specific patterns. Some pseudogene transcripts have intact open reading frames and are translated in cultured cells, representing unannotated protein-coding genes. To assess the biological impact of noncoding pseudogenes, we CRISPR-Cas9 delete the nucleus-enriched pseudogene PDCL3P4 and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the human transcriptional landscape.

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Insights into the Genome Sequence ofChromobacterium amazonenseIsolated from a Tropical Freshwater Lake

International Journal of Genomics ◽

10.1155/2018/1062716 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

Alexandre Bueno Santos ◽

Patrícia Silva Costa ◽

Anderson Oliveira do Carmo ◽

Gabriel da Rocha Fernandes ◽

Larissa Lopes Silva Scholte ◽

...

Keyword(s):

De Novo ◽

Genomic Diversity ◽

Protein Coding ◽

Biotechnological Potential ◽

Draft Assembly ◽

Functional Studies ◽

Alpha Hemolysin ◽

Type Iv ◽

Nudix Hydrolases ◽

Colicin V

Members of the genusChromobacteriumhave been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis ofChromobacterium amazonensestrain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present. The genome also contains a collection of genes of biotechnological interest, including esterases, lipase, auxins, chitinases, phytoene synthase and phytoene desaturase, polyhydroxyalkanoates, violacein, plastocyanin/azurin, and detoxifying compounds. Importantly, unlike otherChromobacteriumspecies, the 56AF genome contains genes for pore-forming toxin alpha-hemolysin, a type IV secretion system, among others. The analysis of theC. amazonensestrain 56AF genome reveals the versatility, adaptability, and biotechnological potential of this bacterium. This study provides molecular information that may pave the way for further comparative genomics and functional studies involvingChromobacterium-related isolates and improves our understanding of the global genomic diversity ofChromobacteriumspecies.

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