The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)

Abstract

BackgroundThe genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca.FindingsIn this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced.ConclusionsComparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca.The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

“…More recently, since the introduction of high-throughput sequencing technologies, the number of genome sequencing projects has increased at an exponential rate, leading to genome assemblies for organisms previously considered too low a priority to be sequenced. For instance, high-quality genome assemblies have been released for Potentilla micrantha (Buti et al, 2017), Salvia splendens (Dong et al, 2018), Cuscuta campestris (Vogel et al, 2018) and Casuarina equisetifolia (Ye et al, 2019).…”

Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

“…The genomes of Potentilla micranthia (Buti et al, 2018), Rubus occidentalis (VanBuren et al, 91 2016), and Fragaria vesca (Edger et al, 2018) were leveraged to improve scaffolding using 92…”

“…A comparative genomic approach (Bosi et al, 2015;189 Pop et al, 2004) was used as part of the genome assembly. Specifically, the most recently 190 assembled genomes of closely related species Potentilla micranthia (Buti et al, 2018), Rubus 191 occidentalis (VanBuren et al, 2016), and Fragaria vesca (Edger et al, 2018) were leveraged to 192 improve scaffolding using MeDuSa (Bosi et al, 2015). The resulting R. idaeus genome assembly 193 is 300 Mbp in size, containing 2,145 scaffolds with a N50 of 638 Kb (Table 1) Table 2).…”

“…Fragaria vesca (woodland strawberry) (Edger et al, 2018;Shulaev et al, 2011), Potentilla 42 micranthia (mock strawberry) (Buti et al, 2018), and Rosa chinensis (Chinese rose) (Hibrand 43 Saint-Oyant et al, 2018;Raymond et al, 2018). Due to the small genome size, wide variety of 44 fruit types (pomes, drupes, achenes, hips, follicles and capsules), and plant growth habits 45 (ranging from herbaceous to cane, bush and tree forms), Rosaceous genomes offer one of the 46 best systems for the comparative studies in genome evolution and development (Xiang et al, 3 2017).…”

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

“…LTR-REs can be classified into two major superfamilies, Gypsy and Copia [19], depending on the order of the enzyme-coding regions within the Pol domain. Superfamilies, on their turn, are subdivided into a number of lineages in relation to their structure and sequence [23][24][25][26][27][28][29].…”