Cargando…
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary datasets. Analysis of this highly contiguous (chromosome-scal...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
2018
|
| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805609/ https://www.ncbi.nlm.nih.gov/pubmed/29358652 http://dx.doi.org/10.1038/s41588-017-0036-1 |
| _version_ | 1783298997224472576 |
|---|---|
| author | Smith, Jeramiah J. Timoshevskaya, Nataliya Ye, Chengxi Holt, Carson Keinath, Melissa C. Parker, Hugo J. Cook, Malcolm E. Hess, Jon E. Narum, Shawn R. Lamanna, Francesco Kaessmann, Henrik Timoshevskiy, Vladimir A. Waterbury, Courtney K. M. Saraceno, Cody Wiedemann, Leanne M. Robb, Sofia M. C. Baker, Carl Eichler, Evan E. Hockman, Dorit Sauka-Spengler, Tatjana Yandell, Mark Krumlauf, Robb Elgar, Greg Amemiya, Chris T. |
| author_facet | Smith, Jeramiah J. Timoshevskaya, Nataliya Ye, Chengxi Holt, Carson Keinath, Melissa C. Parker, Hugo J. Cook, Malcolm E. Hess, Jon E. Narum, Shawn R. Lamanna, Francesco Kaessmann, Henrik Timoshevskiy, Vladimir A. Waterbury, Courtney K. M. Saraceno, Cody Wiedemann, Leanne M. Robb, Sofia M. C. Baker, Carl Eichler, Evan E. Hockman, Dorit Sauka-Spengler, Tatjana Yandell, Mark Krumlauf, Robb Elgar, Greg Amemiya, Chris T. |
| author_sort | Smith, Jeramiah J. |
| collection | PubMed |
| description | The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary datasets. Analysis of this highly contiguous (chromosome-scale) assembly reveals that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by Polycomb Repressive Complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and repressive/bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys’ unique biology and evolutionary/comparative perspective. |
| format | Online Article Text |
| id | pubmed-5805609 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2018 |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-58056092018-07-22 The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution Smith, Jeramiah J. Timoshevskaya, Nataliya Ye, Chengxi Holt, Carson Keinath, Melissa C. Parker, Hugo J. Cook, Malcolm E. Hess, Jon E. Narum, Shawn R. Lamanna, Francesco Kaessmann, Henrik Timoshevskiy, Vladimir A. Waterbury, Courtney K. M. Saraceno, Cody Wiedemann, Leanne M. Robb, Sofia M. C. Baker, Carl Eichler, Evan E. Hockman, Dorit Sauka-Spengler, Tatjana Yandell, Mark Krumlauf, Robb Elgar, Greg Amemiya, Chris T. Nat Genet Article The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary datasets. Analysis of this highly contiguous (chromosome-scale) assembly reveals that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by Polycomb Repressive Complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and repressive/bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys’ unique biology and evolutionary/comparative perspective. 2018-01-22 2018-02 /pmc/articles/PMC5805609/ /pubmed/29358652 http://dx.doi.org/10.1038/s41588-017-0036-1 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms |
| spellingShingle | Article Smith, Jeramiah J. Timoshevskaya, Nataliya Ye, Chengxi Holt, Carson Keinath, Melissa C. Parker, Hugo J. Cook, Malcolm E. Hess, Jon E. Narum, Shawn R. Lamanna, Francesco Kaessmann, Henrik Timoshevskiy, Vladimir A. Waterbury, Courtney K. M. Saraceno, Cody Wiedemann, Leanne M. Robb, Sofia M. C. Baker, Carl Eichler, Evan E. Hockman, Dorit Sauka-Spengler, Tatjana Yandell, Mark Krumlauf, Robb Elgar, Greg Amemiya, Chris T. The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution |
| title | The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution |
| title_full | The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution |
| title_fullStr | The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution |
| title_full_unstemmed | The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution |
| title_short | The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution |
| title_sort | sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805609/ https://www.ncbi.nlm.nih.gov/pubmed/29358652 http://dx.doi.org/10.1038/s41588-017-0036-1 |
| work_keys_str_mv | AT smithjeramiahj thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT timoshevskayanataliya thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT yechengxi thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT holtcarson thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT keinathmelissac thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT parkerhugoj thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT cookmalcolme thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT hessjone thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT narumshawnr thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT lamannafrancesco thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT kaessmannhenrik thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT timoshevskiyvladimira thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT waterburycourtneykm thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT saracenocody thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT wiedemannleannem thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT robbsofiamc thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT bakercarl thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT eichlerevane thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT hockmandorit thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT saukaspenglertatjana thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT yandellmark thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT krumlaufrobb thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT elgargreg thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT amemiyachrist thesealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT smithjeramiahj sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT timoshevskayanataliya sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT yechengxi sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT holtcarson sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT keinathmelissac sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT parkerhugoj sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT cookmalcolme sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT hessjone sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT narumshawnr sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT lamannafrancesco sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT kaessmannhenrik sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT timoshevskiyvladimira sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT waterburycourtneykm sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT saracenocody sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT wiedemannleannem sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT robbsofiamc sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT bakercarl sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT eichlerevane sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT hockmandorit sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT saukaspenglertatjana sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT yandellmark sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT krumlaufrobb sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT elgargreg sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution AT amemiyachrist sealampreygermlinegenomeprovidesinsightsintoprogrammedgenomerearrangementandvertebrateevolution |