Dataset Information

Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences.

ABSTRACT: Despite continuous updates of the human reference genome, there are still hundreds of unresolved gaps which account for about 5% of the total sequence length. Given the availability of whole genome de novo assemblies, especially those derived from long-read sequencing data, gap-closing sequences can be determined. By comparing 17 de novo long-read sequencing assemblies with the human reference genome, we identified a total of 1,125 gap-closing sequences for 132 (16.9% of 783) gaps and added up to 2.2 Mb novel sequences to the human reference genome. More than 90% of the non-redundant sequences could be verified by unmapped reads from the Simons Genome Diversity Project dataset. In addition, 15.6% of the non-reference sequences were found in at least one of four non-human primate genomes. We further demonstrated that the non-redundant sequences had high content of simple repeats and satellite sequences. Moreover, 43 (32.6%) of the 132 closed gaps were shown to be polymorphic; such sequences may play an important biological role and can be useful in the investigation of human genetic diversity.

SUBMITTER: Zhao T

PROVIDER: S-EPMC7407462 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences.

Zhao Tingting T Duan Zhongqu Z Genchev Georgi Z GZ Lu Hui H

G3 (Bethesda, Md.) 20200805 8

Despite continuous updates of the human reference genome, there are still hundreds of unresolved gaps which account for about 5% of the total sequence length. Given the availability of whole genome <i>de novo</i> assemblies, especially those derived from long-read sequencing data, gap-closing sequences can be determined. By comparing 17 <i>de novo</i> long-read sequencing assemblies with the human reference genome, we identified a total of 1,125 gap-closing sequences for 132 (16.9% of 783) gaps ...[more]

PMID: 32532800

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Project description:Global food production needs to be increased by 60-110% between 2005 and 2050 to meet growing food and feed demand. Intensification and/or expansion of agriculture are the two main options available to meet the growing crop demands. Land conversion to expand cultivated land increases GHG emissions and impacts biodiversity and ecosystem services. Closing yield gaps to attain potential yields may be a viable option to increase the global crop production. Traditional methods of agricultural intensification often have negative externalities. Therefore, there is a need to explore location-specific methods of sustainable agricultural intensification. We identified regions where the achievement of potential crop calorie production on currently cultivated land will meet the present and future food demand based on scenario analyses considering population growth and changes in dietary habits. By closing yield gaps in the current irrigated and rain-fed cultivated land, about 24% and 80% more crop calories can respectively be produced compared to 2000. Most countries will reach food self-sufficiency or improve their current food self-sufficiency levels if potential crop production levels are achieved. As a novel approach, we defined specific input and agricultural management strategies required to achieve the potential production by overcoming biophysical and socioeconomic constraints causing yield gaps. The management strategies include: fertilizers, pesticides, advanced soil management, land improvement, management strategies coping with weather induced yield variability, and improving market accessibility. Finally, we estimated the required fertilizers (N, P2O5, and K2O) to attain the potential yields. Globally, N-fertilizer application needs to increase by 45-73%, P2O5-fertilizer by 22-46%, and K2O-fertilizer by 2-3 times compared to the year 2010 to attain potential crop production. The sustainability of such agricultural intensification largely depends on the way management strategies for closing yield gaps are chosen and implemented.

Dataset Information

Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences.

Publications

Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences.

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