Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum
| Autor: | Soon-Chun Jeong, Ji Hong Kim, Myung-Shin Kim, Jeonghun Baek, Taeyoung Lee, Changhoon Kim |
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| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI01140
Glycine max AcademicSubjects/SCI00010 Sequence assembly Locus (genetics) Chromosomal rearrangement Computational biology QH426-470 Biology AcademicSubjects/SCI01180 Genome Structural variation Republic of Korea Genetic variation Genetics genetic map soybean Indel Molecular Biology Gene Alleles Genetics (clinical) fungi structural variation High-Throughput Nucleotide Sequencing food and beverages Fabaceae Genome Report genome assembly AcademicSubjects/SCI00960 Soybeans Reference genome |
| Zdroj: | G3: Genes|Genomes|Genetics G3: Genes, Genomes, Genetics, Vol 11, Iss 10 (2021) |
| Popis: | Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species. |
| Databáze: | OpenAIRE |
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