Fragaria x ananassa Yanli Genome v1.0 Assembly & Annotation

Publication: Mao JX, Wang Y, Wang BT, Li JQ, Zhang C, Zhang WS, Li X, Li J, Zhang JX, Li H, Zhang ZH. High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry. Horticulture Research. Volume 10, Issue 1, January 2023, uhad002, doi: 10.1093/hr/uhad002

Materials and Methods:

Genome assembly

Fragaria x ananassa ‘Yanli’ mature leaves were used for genomic DNA extraction. The quality and concentration of DNA was determined using 1% agarose gel electrophoresis and a Qubit 3.0 fluorometer. PacBio’s standard protocol was used to build SMRTbell target size libraries. The library was sequenced using PacBio Sequel II with primer V2 and Sequel II binding kit 2.0. The de novo assembly was performed using Hifiasm version 0.16.1.

Hi-C assembly

The Illumina HiSeq X Ten platform was used to construct the Hi-C library by anchoring configs onto the chromosome. Qubit 2.0 and Agilent 2100 were used to determine the concentration and insert size. HiCUP was used to process sequence data generated by Hi-C and 3d-DNA was used to assist assembly of genome. After the Hi-C interaction heatmap matrix was constructed by Juicer version 1.5.6, mis-joins, order, and orientation were corrected by JuiceBox version 1.11.08. And the reads were aligned to the genome by Bowtie 2.

Annotation process

A combination of homologue prediction, de novo prediction, and RNA-seq/EST prediction was used to annotate protein-coding genes in the ‘Yanli’ genome. Sequences of Prunus avium, F. vesca, Malus × domestica, Rosa chinensis, and F. × ananassa and Exonerate version 2.2.0 were used for predicting homologous genes. De novo prediction was measured using AUGUSTUS version 3.3.2 and GlimmerHMM version 3.0.4. Splice junctions between exons were identified in the RNA-seq data using TopHat version 2.0.4 and assembled into transcripts using Cufflinks version 2.2.1. All the predictions made using the three methods were combined using MAKER2 version 2.31.10 to generate non-redundant and more complete gene sets. HiCESAP was used for obtaining final reliable gene sets.