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4. Does chromatin diminution affect invertebrate genome assembly?

Author

Komissarov, Aleksey, Kliver, Sergey, Rayko, Mike, Dunham, Joseph P., Iannello, Mariangela, Milani, Liliana, Breton, Sophie, Nuzhdin, Sergey V., Passamonti, Marco, and Ghiselli, Fabrizio

Abstract

The genomics of non-model invertebrates remains challenging. Every step from sampling to final genome annotation has unexpected complications. We sequenced two marine invertebrate genomes: the Manila clam (Ruditapes philippinarum) genome, and the moon jellyfish (Aurelia aurita) genome, using both Illumina and PacBio platforms. We failed to assemble those genomes using all available conventional assemblers or more sophisticated assembly pipelines. Initially we explained this by very high heterozygosity rate and highly repeated genome composition. However during the stage of coverage-wise polishing of PacBio-only assembly by Illumina reads we observed many cases of complex structural variants that cannot be explained by diploid heterozygosity or repeats. After manual check of these regions we found the presence of two types of similar sequences but different in read coverage. We developed a software that analyzes all forks in de Bruijn graphs constructed from Illumina reads and we found that both the clam and the jellyfish genomes additionally to the main 20x coverage have many fragments with a 4x coverage. We manually checked the difference between 20x and 4x fragments finding that they are very similar in sequence but do not have classical heterozygosity difference. We found multiple indels that cannot be explained by Illumina errors or observed natural heterozygosity or by presence of DNA from gametes. We hypothesize that these two genomes are subject to chromatin diminution—a chromosomal fragmentation, followed by the elimination of part of the chromosome during mitosis. We have developed a specific assembly pipeline to trying to solve this issue.

Published
2018
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5. Supplementary – Supplemental material for Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales

Author

Antonets, Kirill S, Kliver, Sergey F, and Nizhnikov, Anton A

Subjects
Cell Biology
Abstract

Supplemental material, Supplementary for Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales by Kirill S Antonets, Sergey F Kliver and Anton A Nizhnikov in Evolutionary Bioinformatics

Published
2018
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6. Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola

Author

Grigorev, Kirill, primary, Kliver, Sergey, additional, Dobrynin, Pavel, additional, Komissarov, Aleksey, additional, Wolfsberger, Walter, additional, Krasheninnikova, Ksenia, additional, Afanador-Hernández, Yashira M, additional, Brandt, Adam L, additional, Paulino, Liz A, additional, Carreras, Rosanna, additional, Rodríguez, Luis E, additional, Núñez, Adrell, additional, Brandt, Jessica R, additional, Silva, Filipe, additional, Hernández-Martich, J David, additional, Majeske, Audrey J, additional, Antunes, Agostinho, additional, Roca, Alfred L, additional, O'Brien, Stephen J, additional, Martínez-Cruzado, Juan Carlos, additional, and Oleksyk, Taras K, additional

Published
2018
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8. Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangeredSolenodon paradoxusfrom the island of Hispaniola

Author

Grigorev, Kirill, primary, Kliver, Sergey, additional, Dobrynin, Pavel, additional, Komissarov, Aleksey, additional, Wolfsberger, Walter, additional, Krasheninnikova, Ksenia, additional, Afanador-Hernández, Yashira M., additional, Paulino, Liz A., additional, Carreras, Rosanna, additional, Rodríguez, Luis E., additional, Núñez, Adrell, additional, Silva, Filipe, additional, Hernández-Martich, J. David, additional, Majeske, Audrey J., additional, Antunes, Agostinho, additional, Roca, Alfred L., additional, O’Brien, Stephen J., additional, Martinez-Cruzado, Juan Carlos, additional, and Oleksyk, Taras K., additional

Published
2017
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9. Additional file 1 of Genomic legacy of the African cheetah, Acinonyx jubatus

Author

Dobrynin, Pavel, Shiping Liu, Gaik Tamazian, Zijun Xiong, Yurchenko, Andrey, Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Küntzel, Anne, Klaus-Peter Koepfli, Johnson, Warren, Kuderna, Lukas, GarcíA-Pérez, Raquel, Manuel, Marc, Godinez, Ricardo, Komissarov, Aleksey, Makunin, Alexey, Brukhin, Vladimir, Weilin Qiu, Zhou, Long, Li, Fang, Yi, Jian, Driscoll, Carlos, Antunes, Agostinho, Oleksyk, Taras, Eizirik, Eduardo, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Guojie Zhang, and O’Brien, Stephen

Abstract

Supplemental figures. Figure S1. Cheetah genome size estimation by 17-mers. Figure S2. Depth distribution of cheetah reads. Figure S3. GC content and average sequencing depth values. Figure S4. Depth distribution of re-sequencing reads. Figure S5. Distribution of syntenic blocks in genome windows. Figure S6. Ten largest cat-cheetah rearrangements. Figure S7. Size of homozygosity stretches in Felidae genomes. Figure S8. Ideograms of homozygosity regions. Figure S9. Comparison of cheetah and human MHC regions. Figure S10. Comparison of cheetah and dog MHC regions. Figure S11. Inferred historical population sizes by PSMC analysis. Figure S12. Bootstrap values for DaDi demographic models. Figure S13. Alignments of the AKAP4 gene. Figure S14. Evolutionary history of LDH gene families. Figure S15. Cumulative distribution of 36-mers. Figure S16. Copy-number distribution in control regions. Figure S17. Example of fixed duplications on scaffold606. (PDF 2027 kb)

Published
2015
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10. Pangolin genomes and the evolution of mammalian scales and immunity

Author

Choo, Siew Woh, primary, Rayko, Mike, additional, Tan, Tze King, additional, Hari, Ranjeev, additional, Komissarov, Aleksey, additional, Wee, Wei Yee, additional, Yurchenko, Andrey A., additional, Kliver, Sergey, additional, Tamazian, Gaik, additional, Antunes, Agostinho, additional, Wilson, Richard K., additional, Warren, Wesley C., additional, Koepfli, Klaus-Peter, additional, Minx, Patrick, additional, Krasheninnikova, Ksenia, additional, Kotze, Antoinette, additional, Dalton, Desire L., additional, Vermaak, Elaine, additional, Paterson, Ian C., additional, Dobrynin, Pavel, additional, Sitam, Frankie Thomas, additional, Rovie-Ryan, Jeffrine J., additional, Johnson, Warren E., additional, Yusoff, Aini Mohamed, additional, Luo, Shu-Jin, additional, Karuppannan, Kayal Vizi, additional, Fang, Gang, additional, Zheng, Deyou, additional, Gerstein, Mark B., additional, Lipovich, Leonard, additional, O'Brien, Stephen J., additional, and Wong, Guat Jah, additional

Published
2016
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11. Genomic legacy of the African cheetah, Acinonyx jubatus

Author

Dobrynin, Pavel, Liu, Shiping, Tamazian, Gaik, Xiong, Zijun, Yurchenko, Andrey A., Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Kuentzel, Anne, Koepfli, Klaus-Peter, Johnson, Warren, Kuderna, Lukas F. K., Garcia-Perez, Raquel, de Manuel, Marc, Godinez, Ricardo, Komissarov, Aleksey, Makunin, Alexey, Brukhin, Vladimir, Qiu, Weilin, Zhou, Long, Li, Fang, Yi, Jian, Driscoll, Carlos, Antunes, Agostinho, Oleksyk, Taras K., Eizirik, Eduardo, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Zhang, Guojie, O'Brien, Stephen J., Dobrynin, Pavel, Liu, Shiping, Tamazian, Gaik, Xiong, Zijun, Yurchenko, Andrey A., Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Kuentzel, Anne, Koepfli, Klaus-Peter, Johnson, Warren, Kuderna, Lukas F. K., Garcia-Perez, Raquel, de Manuel, Marc, Godinez, Ricardo, Komissarov, Aleksey, Makunin, Alexey, Brukhin, Vladimir, Qiu, Weilin, Zhou, Long, Li, Fang, Yi, Jian, Driscoll, Carlos, Antunes, Agostinho, Oleksyk, Taras K., Eizirik, Eduardo, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Zhang, Guojie, and O'Brien, Stephen J.

Published
2015

12. Genomic legacy of the African cheetah, Acinonyx jubatus

Author

Dobrynin, Pavel, primary, Liu, Shiping, additional, Tamazian, Gaik, additional, Xiong, Zijun, additional, Yurchenko, Andrey A., additional, Krasheninnikova, Ksenia, additional, Kliver, Sergey, additional, Schmidt-Küntzel, Anne, additional, Koepfli, Klaus-Peter, additional, Johnson, Warren, additional, Kuderna, Lukas F.K., additional, García-Pérez, Raquel, additional, Manuel, Marc de, additional, Godinez, Ricardo, additional, Komissarov, Aleksey, additional, Makunin, Alexey, additional, Brukhin, Vladimir, additional, Qiu, Weilin, additional, Zhou, Long, additional, Li, Fang, additional, Yi, Jian, additional, Driscoll, Carlos, additional, Antunes, Agostinho, additional, Oleksyk, Taras K., additional, Eizirik, Eduardo, additional, Perelman, Polina, additional, Roelke, Melody, additional, Wildt, David, additional, Diekhans, Mark, additional, Marques-Bonet, Tomas, additional, Marker, Laurie, additional, Bhak, Jong, additional, Wang, Jun, additional, Zhang, Guojie, additional, and O’Brien, Stephen J., additional

Published
2015
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