Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets

Abstract

The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries. Altogether, 18,641 genes (55.6% out of 33,538 genes) were augmented with information on the 5′ and/or 3′ UTRs, 13,168 (39.3%) protein-coding genes were modified or newly identified, and 7,370 genes were found to possess alternative isoforms. In addition, 1,938 long non-coding RNAs, 171 miRNAs, and 51,714 small RNA clusters were integrated into the annotation. This new annotation of F. vesca is substantially improved in both accuracy and integrity of gene predictions, beneficial to the gene functional studies in strawberry and to the comparative genomic analysis of other horticultural crops in Rosaceae family.

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

“…The variation in NBS‐LRR gene content between individuals has been assumed to play an important role in the resistance or susceptibility of crops to disease (Tollenaere et al ., ; Wu et al ., ). Furthermore, we found that the largest class of RGA candidates were RLKs, which has been previously reported in other plants, such as wild strawberry and cotton (Chen et al ., ; Li et al ., ). This frequency might be due to a greater diversity of roles of RLK than RLP and NBS‐LRR genes.…”

Conserved and novel roles of miR164‐CUC2 regulatory module in specifying leaf and floral organ morphology in strawberry

“…The 21nt miR164a mature sequence is located within the first exon, and the SNP (G to A) occurred in its 19 th nucleotide. Based on the prior RNA‐seq data (Li et al ., ), pri‐ FvemiR164A is more abundant in shoot apical meristem (SAM), flower meristem (FM), and receptacle meristem (REM) (Fig. S4a).…”

“…The other two genes are named as FveMIR164B and FveMIR164C . According to the previous RNA‐seq data (Li et al ., ), pri‐ FvemiR164A is more abundant in SAM, FM, and receptacle meristem (REM), while pri‐ FvemiR164B is preferentially accumulated in anthers and fruit receptacles, suggesting that they may function in different tissues and developmental processes. FvemiR164c is expressed at a much lower level (Fig.…”

“…Protein sequences were obtained from the F. vesca genome annotation v.2.0.a2 (Li et al ., ), TAIR (http://www.arabidopsis.org/), and NCBI (https://www.ncbi.nlm.nih.gov/) based on their accession numbers. Sequence alignment was performed using Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo).…”

Apollo: Democratizing genome annotation

“…To date, the i5K Workspace has supported publication of seven insect genomes that were manually curated with Apollo (11)(12)(13)(14)(15)(16)(17). Other projects that have used Apollo include genomes of additional insects (18)(19)(20), human parasites (21)(22)(23), birds (24,25), the sea lamprey (26), plants (27)(28)(29), fungi (30)(31)(32)(33)(34)(35) and a plant pathogenic nematode (36). Projects such as the re-annotation of the whipworm genome by hundreds of high school students in the UK, supported by the Institute for Research in Schools (IRIS) (37), and the curation of 33,044 gene loci in the kiwifruit genome by 93 annotators, are evidence of Apollo's robust support for large dispersed projects.…”