Genome Assembly of Salicaceae Populus deltoides (Eastern Cottonwood) I-69 Based on Nanopore Sequencing and Hi-C Technologies
| العنوان: | Genome Assembly of Salicaceae Populus deltoides (Eastern Cottonwood) I-69 Based on Nanopore Sequencing and Hi-C Technologies |
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| المؤلفون: | Zhiting Li, Chunfa Tong, Wei Zhao, Shengjun Bai, Zhiliang Pan, Jinpeng Zhang, Hainan Wu |
| المصدر: | Journal of Heredity |
| بيانات النشر: | Oxford University Press (OUP), 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | AcademicSubjects/SCI01140, Transposable element, Jhered/6, Genome Resources, Sequence assembly, Biology, Genome, Genetics, chromosome conformation capture technology, Molecular Biology, Gene, Phylogeny, Genetics (clinical), Populus deltoides, Whole genome sequencing, Contig, Molecular Sequence Annotation, biology.organism_classification, body regions, Nanopore Sequencing, Populus, genome assembly, Eastern Cottonwood, Nanopore sequencing, human activities, Genome, Plant, Biotechnology |
| الوصف: | Populus deltoides has important ecological and economic values, widely used in poplar breeding programs due to its superior characteristics such as rapid growth and resistance to disease. Although the genome sequence of P. deltoides WV94 is available, the assembly is fragmented. Here, we reported an improved chromosome-level assembly of the P. deltoides cultivar I-69 by combining Nanopore sequencing and chromosome conformation capture (Hi-C) technologies. The assembly was 429.3 Mb in size and contained 657 contigs with a contig N50 length of 2.62 Mb. Hi-C scaffolding of the contigs generated 19 chromosome-level sequences, which covered 97.4% (418 Mb) of the total assembly size. Moreover, repetitive sequences annotation showed that 39.28% of the P. deltoides genome was composed of interspersed elements, including retroelements (23.66%), DNA transposons (6.83%), and unclassified elements (8.79%). We also identified a total of 44 362 protein-coding genes in the current P. deltoides assembly. Compared with the previous genome assembly of P. deltoides WV94, the current assembly had some significantly improved qualities: the contig N50 increased 3.5-fold and the proportion of gaps decreased from 3.2% to 0.08%. This high-quality, well-annotated genome assembly provides a reliable genomic resource for identifying genome variants among individuals, mining candidate genes that control growth and wood quality traits, and facilitating further application of genomics-assisted breeding in populations related to P. deltoides. |
| تدمد: | 1465-7333 0022-1503 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e17064522e34ba491cbd362ba5ca90f3 https://doi.org/10.1093/jhered/esab010 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....e17064522e34ba491cbd362ba5ca90f3 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14657333 00221503 |
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