Frontiers in Genetics (Sep 2022)
Chromosome-level genome assembly of Fragaria pentaphylla using PacBio and Hi-C technologies
- Rui Sun,
- Rui Sun,
- Rui Sun,
- Shuangtao Li,
- Shuangtao Li,
- Shuangtao Li,
- Linlin Chang,
- Linlin Chang,
- Linlin Chang,
- Jing Dong,
- Jing Dong,
- Jing Dong,
- Chuanfei Zhong,
- Chuanfei Zhong,
- Chuanfei Zhong,
- Hongli Zhang,
- Hongli Zhang,
- Hongli Zhang,
- Lingzhi Wei,
- Lingzhi Wei,
- Lingzhi Wei,
- Yongshun Gao,
- Yongshun Gao,
- Yongshun Gao,
- Guixia Wang,
- Guixia Wang,
- Guixia Wang,
- Yuntao Zhang,
- Yuntao Zhang,
- Yuntao Zhang,
- Jian Sun,
- Jian Sun,
- Jian Sun
Affiliations
- Rui Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Rui Sun
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Rui Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Shuangtao Li
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Shuangtao Li
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Shuangtao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Linlin Chang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Linlin Chang
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Linlin Chang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Jing Dong
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Jing Dong
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Jing Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Chuanfei Zhong
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Chuanfei Zhong
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Chuanfei Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Hongli Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Hongli Zhang
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Hongli Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Lingzhi Wei
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Lingzhi Wei
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Lingzhi Wei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Yongshun Gao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Yongshun Gao
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Yongshun Gao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Guixia Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Guixia Wang
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Guixia Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Yuntao Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Yuntao Zhang
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Yuntao Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Jian Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Jian Sun
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Jian Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- DOI
- https://doi.org/10.3389/fgene.2022.873711
- Journal volume & issue
-
Vol. 13
Abstract
Fragaria pentaphylla, a wild diploid quinquefoliolate species of Fragaria, is native to Southwest China. It has two morphs of red and white fruit color in nature and has characteristics of unique fragrance and resistance, which made it not only a valuable breeding material but also a potential model plant for molecular function researches. Here, we generate a high-quality chromosome-level genome assembly of a F. pentaphylla accession, BAAFS-FP039 employing a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. The assembled genome contained 256.74 Mb and a contig N50 length of 32.38 Mb, accounting for 99.9% of the estimated genome (256.77 Mb). Based on Hi-C data, seven pseudo-chromosomes of F. pentaphylla-FP039 genome were assembled, covering 99.39% of the genome assembly. The genome was composed of 44.61% repetitive sequences and 29,623 protein-coding genes, 97.62% of protein-coding genes could be functionally annotated. Phylogenetic and chromosome syntenic analysis revealed that F. pentaphylla-FP039 was closely related to F. nubicola. This high-quality genome could provides fundamental molecular resources for evolutionary studies, breeding efforts, and exploring the unique biological characteristics of F. pentaphylla.
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