|Analysis Name||Prunus mira Whole Genome v1.0 Assembly & Annotation |
|Method||FALCON, ALLPATHS-LG |
|Source||Prunus mira Illumina and PacBio Reads |
|Date performed||2020-07-14 |
Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation (to be submitted by Cao Ke at Zhengzhou fruit research institute, CAAS, China)
Peach (Prunus persica) is the third most produced fruit crop, and is widely cultivated in temperate and subtropical regions. Due to its small genome size, peach has been used as a model plant for comparative and functional genomic researches of the Rosaceae family. In 2013, a high-quality reference genome sequence of peach constructed with the Sanger whole-genome shotgun approach was released by International Peach Genome Initiative. It is well known that wild germplasm contributes a significant proportion of the genetic resources of major crop species, and significant phenotypic differences in fruit size, flavor, and stress tolerance were found among P. persica and its wild relatives, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. It is necessary to study genetic variations of peach and its wild relatives from a broader perspective, such as pan-genome analyses. P. mira is an attractive model for studying high-altitude adaptability of perennial plants because it originated in the Qinghai-Tibet plateau in China.
Genome facts and statistics
The high-quality genome of P. mira was assembled using a more than 100-years old tree through a combination of PacBio, Illumina, and Hi-C (High-throughput chromosome conformation capture) platforms. After estimating the genome size using the k-mer method, a total of 597.0× coverage of sequences were generated and used for genome assembly.
Illumina reads from the wild specie were assembled using ALLPATHS-LG, and gaps in the assemblies were filled using GapCloser V1.12. Mate-paired reads were then used to generate scaffolds using SSPACE. In additon, PacBio SMRT reads were de novo assembled using FALCON. Approximately 13.93 Gb of PacBio SMRT reads were first pairwise compared, and the longest 60 coverage of subreads were selected as seeds to do error correction. All PacBio SMRT reads were mapped back to the assembled contigs with Blast and the Arrow program implemented in SMRT Link (PacBio) was used for error correction with default parameters. The Illumina paired-end reads were then mapped to the corrected contigs to perform the second round of error correction. To further improve the continuity of the assembly, SSPACE (v3.0) was used to build scaffolds using reads from all the mate pair libraries. FragScaff v1-1 was further applied to build superscaffolds using the barcoded sequencing reads. Finally, Hi-C data were used to correct superscaffolds and cluster the scaffolds into pseudochromosomes. A total of 657 scaffolds were anchored and 93.4% of them were allocated to eight pseudochromosomes. The contig N50 and scaffold N50 sizes of the final assembly were 443.7 kb and 27.44 Mb, respectively.
Gene prediction was performed using a combination of homology, ab initio and transcriptome based approaches resulting in 28,943 protein-coding genes in P. mira.
All assembly and annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar. Each data type page will provide a description of the available files and links to download. Alternatively, you can browse all available files on the FTP repository.
The Prunus mira Genome v1.0 assembly file is available in FASTA format.
|Chromosomes (FASTA file)
The Prunus mira v1.0 genome gene prediction files are available in FASTA and GFF3 formats.
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Prunus mira genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.