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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen, Tarjei S. ; Broad Institute Genome Sequencing Platform ; Wakefield, Matthew J. ; [et al.]

Springer Science and Business Media LLC ; 2007

In: Nature Vol. 447, No. 7141 ( 2007-5), p. 167-177

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In: Nature, Springer Science and Business Media LLC, Vol. 447, No. 7141 ( 2007-5), p. 167-177

Type of Medium: Online Resource

ISSN: 0028-0836 , 1476-4687

URL: Article

DOI: 10.1038/nature05805

RVK:

TA 1000

RVK:

UA 1000

RVK:

WA 15000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2007

detail.hit.zdb_id: 120714-3

detail.hit.zdb_id: 1413423-8

SSG: 11

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The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Bradley Shaffer, H ; Minx, Patrick ; Warren, Daniel E ; [et al.]

Springer Science and Business Media LLC ; 2013

In: Genome Biology Vol. 14, No. 3 ( 2013), p. R28-

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In: Genome Biology, Springer Science and Business Media LLC, Vol. 14, No. 3 ( 2013), p. R28-

Type of Medium: Online Resource

ISSN: 1465-6906

URL: Article

DOI: 10.1186/gb-2013-14-3-r28

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2013

detail.hit.zdb_id: 2040529-7

SSG: 12

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The African coelacanth genome provides insights into tetrapod evolution

Amemiya, Chris T. ; Alföldi, Jessica ; Lee, Alison P. ; [et al.]

Springer Science and Business Media LLC ; 2013

In: Nature Vol. 496, No. 7445 ( 2013-4), p. 311-316

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In: Nature, Springer Science and Business Media LLC, Vol. 496, No. 7445 ( 2013-4), p. 311-316

Type of Medium: Online Resource

ISSN: 0028-0836 , 1476-4687

URL: Article

DOI: 10.1038/nature12027

RVK:

TA 1000

RVK:

UA 1000

RVK:

WA 15000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2013

detail.hit.zdb_id: 120714-3

detail.hit.zdb_id: 1413423-8

SSG: 11

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Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility

Nuttle, Xander ; Giannuzzi, Giuliana ; Duyzend, Michael H. ; [et al.]

Springer Science and Business Media LLC ; 2016

In: Nature Vol. 536, No. 7615 ( 2016-8), p. 205-209

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In: Nature, Springer Science and Business Media LLC, Vol. 536, No. 7615 ( 2016-8), p. 205-209

Type of Medium: Online Resource

ISSN: 0028-0836 , 1476-4687

URL: Article

DOI: 10.1038/nature19075

RVK:

TA 1000

RVK:

UA 1000

RVK:

WA 15000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 120714-3

detail.hit.zdb_id: 1413423-8

SSG: 11

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African Lungfish Reveal the Evolutionary Origins of Organized Mucosal Lymphoid Tissue in Vertebrates

Tacchi, Luca ; Larragoite, Erin T. ; Muñoz, Pilar ; [et al.]

Elsevier BV ; 2015

In: Current Biology Vol. 25, No. 18 ( 2015-09), p. 2417-2424

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In: Current Biology, Elsevier BV, Vol. 25, No. 18 ( 2015-09), p. 2417-2424

Type of Medium: Online Resource

ISSN: 0960-9822

URL: Article

DOI: 10.1016/j.cub.2015.07.066

Language: English

Publisher: Elsevier BV

Publication Date: 2015

detail.hit.zdb_id: 2019214-9

SSG: 12

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Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour

Deakin, Janine E. ; Bender, Hannah S. ; Pearse, Anne-Maree ; [et al.]

Public Library of Science (PLoS) ; 2012

In: PLoS Genetics Vol. 8, No. 2 ( 2012-2-16), p. e1002483-

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In: PLoS Genetics, Public Library of Science (PLoS), Vol. 8, No. 2 ( 2012-2-16), p. e1002483-

Type of Medium: Online Resource

ISSN: 1553-7404

URL: Article

DOI: 10.1371/journal.pgen.1002483

DOI: 10.1371/journal.pgen.1002483.g001

DOI: 10.1371/journal.pgen.1002483.g002

DOI: 10.1371/journal.pgen.1002483.g003

DOI: 10.1371/journal.pgen.1002483.g004

DOI: 10.1371/journal.pgen.1002483.g005

DOI: 10.1371/journal.pgen.1002483.g006

DOI: 10.1371/journal.pgen.1002483.g007

DOI: 10.1371/journal.pgen.1002483.g008

DOI: 10.1371/journal.pgen.1002483.t001

DOI: 10.1371/journal.pgen.1002483.t002

DOI: 10.1371/journal.pgen.1002483.t003

DOI: 10.1371/journal.pgen.1002483.s001

DOI: 10.1371/journal.pgen.1002483.s002

DOI: 10.1371/journal.pgen.1002483.s003

DOI: 10.1371/journal.pgen.1002483.s004

DOI: 10.1371/journal.pgen.1002483.s005

DOI: 10.1371/journal.pgen.1002483.s006

DOI: 10.1371/journal.pgen.1002483.s007

DOI: 10.1371/journal.pgen.1002483.s008

DOI: 10.1371/journal.pgen.1002483.s009

DOI: 10.1371/journal.pgen.1002483.s010

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2012

detail.hit.zdb_id: 2186725-2

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Resolution of the novel immune-type receptor gene cluster in zebrafish

Yoder, Jeffrey A. ; Litman, Ronda T. ; Mueller, M. Gail ; [et al.]

Proceedings of the National Academy of Sciences ; 2004

In: Proceedings of the National Academy of Sciences Vol. 101, No. 44 ( 2004-11-02), p. 15706-15711

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 101, No. 44 ( 2004-11-02), p. 15706-15711

Abstract: The novel immune-type receptor (NITR) genes encode a unique multigene family of leukocyte regulatory receptors, which possess an extracellular Ig variable (V) domain and may function in innate immunity. Artificial chromosomes that encode zebrafish NITRs have been assembled into a contig spanning ≈350 kb. Resolution of the complete NITR gene cluster has led to the identification of eight previously undescribed families of NITRs and has revealed the presence of C-type lectins within the locus. A maximum haplotype of 36 NITR genes (138 gene sequences in total) can be grouped into 12 distinct families, including inhibitory and activating receptors. An extreme level of interindividual heterozygosity is reflected in allelic polymorphisms, haplotype variation, and family-specific isoform complexity. In addition, the exceptional diversity of NITR sequences among species suggests divergent evolution of this multigene family with a birth-and-death process of member genes. High-confidence modeling of Nitr V-domain structures reveals a significant shift in the spatial orientation of the Ig fold, in the region of highest interfamily variation, compared with Ig V domains. These studies resolve a complete immune gene cluster in zebrafish and indicate that the NITRs represent the most complex family of activating/inhibitory surface receptors thus far described.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.0405242101

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2004

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Braasch, Ingo ; Gehrke, Andrew R ; Smith, Jeramiah J ; [et al.]

Springer Science and Business Media LLC ; 2016

In: Nature Genetics Vol. 48, No. 4 ( 2016-04), p. 427-437

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 48, No. 4 ( 2016-04), p. 427-437

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/ng.3526

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 1494946-5

SSG: 12

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A novel multigene family encodes diversified variable regions

Strong, Scott J. ; Mueller, M. Gail ; Litman, Ronda T. ; [et al.]

Proceedings of the National Academy of Sciences ; 1999

In: Proceedings of the National Academy of Sciences Vol. 96, No. 26 ( 1999-12-21), p. 15080-15085

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 96, No. 26 ( 1999-12-21), p. 15080-15085

Abstract: Antigen recognition in the adaptive immune response by Ig and T-cell antigen receptors (TCRs) is effected through patterned differences in the peptide sequence in the V regions. V-region specificity forms through genetically programmed rearrangement of individual, diversified segmental elements in single somatic cells. Other Ig superfamily members, including natural killer receptors that mediate cell-surface recognition, do not undergo segmental reorganization, and contain type-2 C (C2) domains, which are structurally distinct from the C1 domains found in Ig and TCR. Immunoreceptor tyrosine-based inhibitory motifs that transduce negative regulatory signals through the cell membrane are found in certain natural killer and other cell surface inhibitory receptors, but not in Ig and TCR. In this study, we employ a genomic approach by using the pufferfish ( Spheroides nephelus ) to characterize a nonrearranging novel immune-type receptor gene family. Twenty-six different nonrearranging genes, which each encode highly diversified V as well as a V-like C2 extracellular domain, a transmembrane region, and in most instances, an immunoreceptor tyrosine-based inhibitory motif-containing cytoplasmic tail, are identified in an ≈113 kb P1 artificial chromosome insert. The presence in novel immune-type receptor genes of V regions that are related closely to those found in Ig and TCR as well as regulatory motifs that are characteristic of inhibitory receptors implies a heretofore unrecognized link between known receptors that mediate adaptive and innate immune functions.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.96.26.15080

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 1999

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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A genome-wide assessment of the ancestral neural crest gene regulatory network

Hockman, Dorit ; Chong-Morrison, Vanessa ; Green, Stephen A. ; [et al.]

Springer Science and Business Media LLC ; 2019

In: Nature Communications Vol. 10, No. 1 ( 2019-10-16)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2019-10-16)

Abstract: The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis -regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox- α 2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-019-12687-4

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2019

detail.hit.zdb_id: 2553671-0

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