A chromosome-level genome assembly of Plantago ovata

Abstract

Plantago ovata is cultivated for production of its seed husk (psyllium). When wet, the husk transforms into a mucilage with properties suitable for pharmaceutical industries, utilised in supplements for controlling blood cholesterol levels, and food industries for making gluten-free products. There has been limited success in improving husk quantity and quality through breeding approaches, partly due to the lack of a reference genome. Here we constructed the first chromosome-scale reference assembly of P. ovata using a combination of 5.98 million PacBio and 636.5 million Hi-C reads. We also used corrected PacBio reads to estimate genome size and transcripts to generate gene models. The final assembly covers ~ 500 Mb with 99.3% gene set completeness. A total of 97% of the sequences are anchored to four chromosomes with an N50 of ~ 128.87 Mb. The P. ovata genome contains 61.90% repeats, where 40.04% are long terminal repeats. We identified 41,820 protein-coding genes, 411 non-coding RNAs, 108 ribosomal RNAs, and 1295 transfer RNAs. This genome will provide a resource for plant breeding programs to, for example, reduce agronomic constraints such as seed shattering, increase psyllium yield and quality, and overcome crop disease susceptibility.

Figure 1

Plantago ovata. (a) A two-and-a-half-month-old plant. (b) Capsules containing two seeds each are fully ripened and shatter easily at around 25 days post anthesis (DPA).

Figure 2

Gene density (blue), TE (Class I and II) density (purple), % GC (red), distribution of 5S (blue arrows) and 45S (green arrows) rRNA in the P. ovata genome. The figure was generated in R using the karyoploteR library. The x-axis represents genome position (Mb) and the y-axis represents gene density using a sliding window of one megabase in length.

Figure 3

Comparative genomic analyses between P. ovata (PO) with other Laminales species (GA, Genlisea aurea; AM, Antirrhinum majus; EG, Erythranthe guttata; SA, Striga asiatica; PJ, Phtheirospermum japonicum; HI, Handroanthus impetiginosus; SI, Sesamum indicum), one Brassicales (AT, Arabidopsis thaliana) and one Solanales (SL, Solanum lycopersicum). (A) Bar charts for each species in B & C were aligned to the corresponding species in the species tree. Bootstrap values of the species tree of each node are one except N3 is 0.76. (B) Percentage of genes from each species assigned to orthogroups. (C) The number of species-specific orthogroups. (D) Venn diagrams of orthogroups from 7 species (GA, PO, AM, EG, SI, and AT). (E) The number of gene duplication events per internal and terminal nodes from the species-based-phylogenetic tree. (F) Pairwise synteny comparison between P. ovata and A. majus.

Figure 4

A phylogenetic tree of GT61 protein sequences from selected species was visualised using FigTree v1.4.4. Clades A—C were labelled as per Anders et al. and Voiniciuc et al..

Figure 5

Illustration of the genome assembly strategy.