Results 11 to 20 of about 188,459 (209)

Telomere-to-telomere assembly of diploid chromosomes with Verkko

Nature Biotechnology, 2023
The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high ...
Mikko Rautiainen, S. Nurk, B. Walenz, Glennis A. Logsdon, D. Porubsky, A. Rhie, E. Eichler, A. Phillippy, S. Koren   +8 more
semanticscholar   +1 more source

Haplotype-resolved assembly of diploid genomes without parental data

Nature Biotechnology, 2022
Routine haplotype-resolved genome assembly from single samples remains an unresolved problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the ...
Haoyu Cheng, E. Jarvis, O. Fedrigo, Klaus‐Peter Koepfli, L. Urban, N. Gemmell, Heng Li   +6 more
semanticscholar   +1 more source

Semi-automated assembly of high-quality diploid human reference genomes

Nature, 2022
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend ...
E. Jarvis, G. Formenti, A. Rhie, Andrea Guarracino, Chentao Yang, J. Wood, A. Tracey, F. Thibaud-Nissen, Mitchell R. Vollger, D. Porubsky, Haoyu Cheng, Mobin Asri, Glennis A. Logsdon, P. Carnevali, Mark J. P. Chaisson, C. Chin, Sarah Cody, J. Collins, Peter Ebert, Merly Escalona, O. Fedrigo, R. Fulton, L. Fulton, S. Garg, Jay Ghurye, E. Green, Ira M. Hall, W. Harvey, Patrick Hasenfeld, A. Hastie, Marina Haukness, Miten Jain, Melanie Kirsche, M. Kolmogorov, J. Korbel, S. Koren, J. Korlach, Joyce Lee, Daofeng Li, Tina Lindsay, Julian K. Lucas, F. Luo, T. Marschall, Jennifer McDaniel, Fan Nie, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, D. Puiu, A. Regier, Jue Ruan, S. Salzberg, A. Sanders, M. Schatz, A. Schmitt, Valerie A. Schneider, Siddarth Selvaraj, Kishwar Shafin, Alaina Shumate, Catherine Stober, J. Torrance, Justin Wagner, Jianxin Wang, A. Wenger, Chuan-Le Xiao, A. Zimin, Guojie Zhang, Ting Wang, Heng Li, Erik K. Garrison, D. Haussler, J. Zook, E. Eichler, A. Phillippy, B. Paten, K. Howe, K. Miga   +76 more
semanticscholar   +1 more source

A nonS-locus F-box gene breaks self-incompatibility in diploid potatoes

Nature Communications, 2021
Potato is the third most important staple food crop. To address challenges associated with global food security, a hybrid potato breeding system, aimed at converting potato from a tuber-propagated tetraploid crop into a seed-propagated diploid crop ...
Ling Ma, Chunzhi Zhang, Bo Zhang, Fei Tang, Futing Li, Qinggang Liao, Dié Tang, Zhen Peng, Yuhong Jia, Meng Gao, Han Guo, Jinzhe Zhang, Xuming Luo, Huiqin Yang, D. Gao, W. J. Lucas, Canhui Li, Sanwen Huang, Y. Shang   +18 more
semanticscholar   +1 more source

Transcriptome and metabolome profiling provide insights into hormone-mediated enhanced growth in autotetraploid seedlings of banana (Musa spp.)

Frontiers in Sustainable Food Systems, 2023
IntroductionReconstructive breeding based on autotetraploids to generate triploid varieties is a promising breeding strategy in banana (Musa spp.).
Ni Zhan, Ni Zhan, Li Li, Li Li, Liping Zhang, Weidi He, Qiaosong Yang, Fangcheng Bi, Guiming Deng, Andrew Kiggundu, Ganjun Yi, Ou Sheng   +11 more
doaj   +1 more source

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

bioRxiv, 2020
Motivation With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible.
Davide Heller, M. Vingron
semanticscholar   +1 more source

Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha

eLife, 2021
Eukaryotic life cycles alternate between haploid and diploid phases and in phylogenetically diverse unicellular eukaryotes, expression of paralogous homeodomain genes in gametes primes the haploid-to-diploid transition.
Tom Dierschke, Edurado Flores-Sondoval, Madlen I. Rast-Somssich, Felix Althoff, S. Zachgo, J. Bowman   +5 more
semanticscholar   +1 more source

Recombinant Diploid Saccharomyces cerevisiae Strain Development for Rapid Glucose and Xylose Co-Fermentation

Fermentation, 2018
Cost-effective production of cellulosic ethanol requires robust microorganisms for rapid co-fermentation of glucose and xylose. This study aims to develop a recombinant diploid xylose-fermenting Saccharomyces cerevisiae strain for efficient conversion of
Tingting Liu, Shuangcheng Huang, Anli Geng   +2 more
doaj   +1 more source

Transcriptome Profiling to Dissect the Role of Genome Duplication on Graft Compatibility Mechanisms in Watermelon

Biology, 2022
Watermelon (Citrullus lanatus) is a popular crop worldwide. Compared to diploid seeded watermelon, triploid seedless watermelon cultivars are in great demand. Grafting in triploid and tetraploid watermelon produces few seedlings.
Mohamed Omar Kaseb, Muhammad Jawad Umer, Muhammad Anees, Hongju Zhu, Shengjie Zhao, Xuqiang Lu, Nan He, Eman El-Remaly, Ahmed El-Eslamboly, Ahmed F. Yousef, Ehab A. A. Salama, Abdulwahed Fahad Alrefaei, Hazem M. Kalaji, Wenge Liu   +13 more
doaj   +1 more source

Haplotype-resolved genome analyses of a heterozygous diploid potato

Nature Genetics, 2020
Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding ...
Qian Zhou, Dié Tang, Wu Huang, Zhongmin Yang, Yu Zhang, J. Hamilton, R. Visser, C. Bachem, C. Robin Buell, Zhonghua Zhang, Chunzhi Zhang, Sanwen Huang   +11 more
semanticscholar   +1 more source