An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes
Summary: Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven chall...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-03-01
|
| Series: | Cell Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124723002747 |
| _version_ | 1827987866578321408 |
|---|---|
| author | Nataliya Timoshevskaya Kaan İ. Eşkut Vladimir A. Timoshevskiy Sofia M.C. Robb Carson Holt Jon E. Hess Hugo J. Parker Cindy F. Baker Allison K. Miller Cody Saraceno Mark Yandell Robb Krumlauf Shawn R. Narum Ralph T. Lampman Neil J. Gemmell Jacquelyn Mountcastle Bettina Haase Jennifer R. Balacco Giulio Formenti Sarah Pelan Ying Sims Kerstin Howe Olivier Fedrigo Erich D. Jarvis Jeramiah J. Smith |
| author_facet | Nataliya Timoshevskaya Kaan İ. Eşkut Vladimir A. Timoshevskiy Sofia M.C. Robb Carson Holt Jon E. Hess Hugo J. Parker Cindy F. Baker Allison K. Miller Cody Saraceno Mark Yandell Robb Krumlauf Shawn R. Narum Ralph T. Lampman Neil J. Gemmell Jacquelyn Mountcastle Bettina Haase Jennifer R. Balacco Giulio Formenti Sarah Pelan Ying Sims Kerstin Howe Olivier Fedrigo Erich D. Jarvis Jeramiah J. Smith |
| author_sort | Nataliya Timoshevskaya |
| collection | DOAJ |
| description | Summary: Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven challenging due to a high content of repeats and gene duplications in eliminated sequences and a corresponding lack of highly accurate and contiguous assemblies for these regions. Here, we present an improved assembly of the sea lamprey (Petromyzon marinus) genome that was generated using recently standardized methods that increase the contiguity and accuracy of vertebrate genome assemblies. This assembly resolves highly contiguous, somatically retained chromosomes and at least one germline-specific chromosome, permitting new analyses that reconstruct the timing, mode, and repercussions of recruitment of genes to the germline-specific fraction. These analyses reveal major roles of interchromosomal segmental duplication, intrachromosomal duplication, and positive selection for germline functions in the long-term evolution of germline-specific chromosomes. |
| first_indexed | 2024-04-09T23:54:48Z |
| format | Article |
| id | doaj.art-8eedbc68b1b441c3b322f413f3b4b86d |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-04-09T23:54:48Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-8eedbc68b1b441c3b322f413f3b4b86d2023-03-17T04:32:59ZengElsevierCell Reports2211-12472023-03-01423112263An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomesNataliya Timoshevskaya0Kaan İ. Eşkut1Vladimir A. Timoshevskiy2Sofia M.C. Robb3Carson Holt4Jon E. Hess5Hugo J. Parker6Cindy F. Baker7Allison K. Miller8Cody Saraceno9Mark Yandell10Robb Krumlauf11Shawn R. Narum12Ralph T. Lampman13Neil J. Gemmell14Jacquelyn Mountcastle15Bettina Haase16Jennifer R. Balacco17Giulio Formenti18Sarah Pelan19Ying Sims20Kerstin Howe21Olivier Fedrigo22Erich D. Jarvis23Jeramiah J. Smith24Department of Biology, University of Kentucky, Lexington, KY 40506, USADepartment of Biology, University of Kentucky, Lexington, KY 40506, USADepartment of Biology, University of Kentucky, Lexington, KY 40506, USAStowers Institute for Medical Research, Kansas City, MO 64110, USADepartment of Human Genetics, University of Utah, Salt Lake City, UT 84112, USAColumbia River Inter-Tribal Fish Commission, Portland, OR 97232, USAStowers Institute for Medical Research, Kansas City, MO 64110, USANational Institute of Water and Atmospheric Research Limited (NIWA), Hamilton, Waikato 3261, New ZealandDepartment of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Otago 9054, New ZealandDepartment of Biology, University of Kentucky, Lexington, KY 40506, USADepartment of Human Genetics, University of Utah, Salt Lake City, UT 84112, USAStowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy & Cell Biology, The University of Kansas School of Medicine, Kansas City, KS 66160, USAColumbia River Inter-Tribal Fish Commission, Hagerman, ID 83332, USAYakama Nation Fisheries Resource Management Program, Pacific Lamprey Project, Toppenish, WA 98948, USADepartment of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Otago 9054, New ZealandVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USAVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USAVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USAVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USATree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UKTree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UKTree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UKVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USAVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USADepartment of Biology, University of Kentucky, Lexington, KY 40506, USA; Corresponding authorSummary: Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven challenging due to a high content of repeats and gene duplications in eliminated sequences and a corresponding lack of highly accurate and contiguous assemblies for these regions. Here, we present an improved assembly of the sea lamprey (Petromyzon marinus) genome that was generated using recently standardized methods that increase the contiguity and accuracy of vertebrate genome assemblies. This assembly resolves highly contiguous, somatically retained chromosomes and at least one germline-specific chromosome, permitting new analyses that reconstruct the timing, mode, and repercussions of recruitment of genes to the germline-specific fraction. These analyses reveal major roles of interchromosomal segmental duplication, intrachromosomal duplication, and positive selection for germline functions in the long-term evolution of germline-specific chromosomes.http://www.sciencedirect.com/science/article/pii/S2211124723002747CP: Molecular biology |
| spellingShingle | Nataliya Timoshevskaya Kaan İ. Eşkut Vladimir A. Timoshevskiy Sofia M.C. Robb Carson Holt Jon E. Hess Hugo J. Parker Cindy F. Baker Allison K. Miller Cody Saraceno Mark Yandell Robb Krumlauf Shawn R. Narum Ralph T. Lampman Neil J. Gemmell Jacquelyn Mountcastle Bettina Haase Jennifer R. Balacco Giulio Formenti Sarah Pelan Ying Sims Kerstin Howe Olivier Fedrigo Erich D. Jarvis Jeramiah J. Smith An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes Cell Reports CP: Molecular biology |
| title | An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes |
| title_full | An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes |
| title_fullStr | An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes |
| title_full_unstemmed | An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes |
| title_short | An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes |
| title_sort | improved germline genome assembly for the sea lamprey petromyzon marinus illuminates the evolution of germline specific chromosomes |
| topic | CP: Molecular biology |
| url | http://www.sciencedirect.com/science/article/pii/S2211124723002747 |
| work_keys_str_mv | AT nataliyatimoshevskaya animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT kaanieskut animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT vladimiratimoshevskiy animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT sofiamcrobb animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT carsonholt animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jonehess animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT hugojparker animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT cindyfbaker animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT allisonkmiller animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT codysaraceno animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT markyandell animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT robbkrumlauf animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT shawnrnarum animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT ralphtlampman animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT neiljgemmell animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jacquelynmountcastle animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT bettinahaase animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jenniferrbalacco animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT giulioformenti animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT sarahpelan animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT yingsims animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT kerstinhowe animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT olivierfedrigo animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT erichdjarvis animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jeramiahjsmith animprovedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT nataliyatimoshevskaya improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT kaanieskut improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT vladimiratimoshevskiy improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT sofiamcrobb improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT carsonholt improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jonehess improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT hugojparker improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT cindyfbaker improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT allisonkmiller improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT codysaraceno improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT markyandell improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT robbkrumlauf improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT shawnrnarum improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT ralphtlampman improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT neiljgemmell improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jacquelynmountcastle improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT bettinahaase improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jenniferrbalacco improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT giulioformenti improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT sarahpelan improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT yingsims improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT kerstinhowe improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT olivierfedrigo improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT erichdjarvis improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes AT jeramiahjsmith improvedgermlinegenomeassemblyforthesealampreypetromyzonmarinusilluminatestheevolutionofgermlinespecificchromosomes |