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A de novo genome assembly of the dwarfing pear rootstock Zhongai 1.

ABSTRACT: 'Zhongai 1' [(Pyrus ussuriensis?×?communis)?×?spp.] is an excellent pear dwarfing rootstock common in China. It is dwarf itself and has high dwarfing efficiency on most of main Pyrus cultivated species when used as inter-stock. Here we describe the draft genome sequences of 'Zhongai 1' which was assembled using PacBio long reads, Illumina short reads and Hi-C technology. We estimated the genome size is approximately 511.33?Mb by K-mer analysis and obtained a final genome of 510.59?Mb with a contig N50 size of 1.28?Mb. Next, 506.31?Mb (99.16%) of contigs were clustered into 17 chromosomes with a scaffold N50 size of 23.45?Mb. We further predicted 309.86?Mb (60.68%) of repetitive sequences and 43,120 protein-coding genes. The assembled genome will be a valuable resource and reference for future pear breeding, genetic improvement, and comparative genomics among related species. Moreover, it will help identify genes involved in dwarfism, early flowering, stress tolerance, and commercially desirable fruit characteristics.

SUBMITTER: Ou C

PROVIDER: S-EPMC6877535 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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A de novo genome assembly of the dwarfing pear rootstock Zhongai 1.

Ou Chunqing C Wang Fei F Wang Jiahong J Li Song S Zhang Yanjie Y Fang Ming M Ma Li L Zhao Yanan Y Jiang Shuling S

Scientific data 20191125 1

'Zhongai 1' [(Pyrus ussuriensis × communis) × spp.] is an excellent pear dwarfing rootstock common in China. It is dwarf itself and has high dwarfing efficiency on most of main Pyrus cultivated species when used as inter-stock. Here we describe the draft genome sequences of 'Zhongai 1' which was assembled using PacBio long reads, Illumina short reads and Hi-C technology. We estimated the genome size is approximately 511.33 Mb by K-mer analysis and obtained a final genome of 510.59 Mb with a cont ...[more]

PMID: 31767847

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Project description:MotivationThere are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage. It is not uncommon that assembly methods involving the overlap graph model are not able to successfully compute greater data sets, mainly due to memory limitation of a computer. This was the reason for developing in last decades mainly de Bruijn-based assembly methods, fast and fairly accurate. However, the latter methods can fail for longer or more repetitive genomes, as they decompose reads to shorter fragments and lose a part of information. An efficient assembler for processing big data sets and using the overlap graph model is still looked out.ResultsWe propose a new genome-scale de novo assembler based on the overlap graph approach, designed for short-read sequencing data. The method, ALGA, incorporates several new ideas resulting in more exact contigs produced in short time. Among these ideas we have creation of a sparse but quite informative graph, reduction of the graph including a procedure referring to the problem of minimum spanning tree of a local subgraph, and graph traversal connected with simultaneous analysis of contigs stored so far. What is rare in genome assembly, the algorithm is almost parameter-free, with only one optional parameter to be set by a user. ALGA was compared with nine state-of-the-art assemblers in tests on genome-scale sequencing data obtained from real experiments on six organisms, differing in size, coverage, GC content, and repetition rate. ALGA produced best results in the sense of overall quality of genome reconstruction, understood as a good balance between genome coverage, accuracy, and length of resulting sequences. The algorithm is one of tools involved in processing data in currently realized national project Genomic Map of Poland.AvailabilityALGA is available at http://alga.put.poznan.pl.Supplementary informationSupplementary material is available at Bioinformatics online.

Dataset Information

A de novo genome assembly of the dwarfing pear rootstock Zhongai 1.

Publications

A de novo genome assembly of the dwarfing pear rootstock Zhongai 1.

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