Journal
G3-GENES GENOMES GENETICS
Volume 10, Issue 10, Pages 3565-3574Publisher
OXFORD UNIV PRESS INC
DOI: 10.1534/g3.120.401532
Keywords
Chinese chestnut; Castanea mollissimaBlume; genome assembly; single molecular sequencing; high-throughput chromosome conformation capture
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Funding
- Agricultural science and technology innovation project of Shandong Academy of Agricultural Science [CXGC2016B07, CXGC2018F03, CXGC2016A03]
- Shandong Provincial Key Laboratory for Fruit Biotechnology Breeding [2018KF03]
- Shandong Provincial Seed Improvement Project [2016LZGC012]
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The Chinese chestnut (Castanea mollissimaBl.) is a woody nut crop with a high ecological value. Although many cultivars have been selected from natural seedlings, elite lines with comprehensive agronomic traits and characters remain rare. To explore genetic resources with aid of whole genome sequence will play important roles in modern breeding programs for chestnut. In this study, we generated a high-qualityC. mollissimagenome assembly by combining 90x Pacific Biosciences long read and 170x high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in theC. mollissimagenome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr development in the Chinese chestnut. This highly contiguous assembly of theC. mollissimagenome provides a valuable resource for studies aiming at identifying and characterizing agronomical-important traits, and will aid the design of breeding strategies to develop more focused, faster, and predictable improvement programs.
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