The Boechera Genus as a Resource for Apomixis Research

Abstract

The genera Boechera (A. Löve et D. Löve) and Arabidopsis, the latter containing the model plant Arabidopsis thaliana, belong to the same clade within the Brassicaceae family. Boechera is the only among the more than 370 genera in the Brassicaceae where apomixis is well documented. Apomixis refers to the asexual reproduction through seed, and a better understanding of the underlying mechanisms has great potential for applications in agriculture. The Boechera genus currently includes 110 species (of which 38 are reported to be triploid and thus apomictic), which are distributed mostly in the North America. The apomictic lineages of Boechera occur at both the diploid and triploid level and show signs of a hybridogenic origin, resulting in a modification of their chromosome structure, as reflected by alloploidy, aneuploidy, substitutions of homeologous chromosomes, and the presence of aberrant chromosomes. In this review, we discuss the advantages of the Boechera genus to study apomixis, consider its modes of reproduction as well as the inheritance and possible mechanisms controlling apomixis. We also consider population genetic aspects and a possible role of hybridization at the origin of apomixis in Boechera. The molecular tools available to study Boechera, such as transformation techniques, laser capture microdissection, analysis of transcriptomes etc. are also discussed. We survey available genome assemblies of Boechera spp. and point out the challenges to assemble the highly heterozygous genomes of apomictic species. Due to these challenges, we argue for the application of an alternative reference-free method for the comparative analysis of such genomes, provide an overview of genomic sequencing data in the genus Boechera suitable for such analysis, and provide examples of its application.

Keywords: Boechera; apomeiosis; apomixis; diplospory; genome assembly; genomics; heterozygosity; pseudogamy.

FIGURE 1

Boechera stricta grown in the greenhouse of the Department of Plant and Microbial Biology of the University of Zurich.

FIGURE 2

Meiotic (sexual) megasporogenesis in ovules of B. holboellii s. l. (A) megaspore mother cell (MMC), nucellus (N); (B,C) tetrad of the megaspores (TMS), the functional megaspore (FMS) at the chalazal end; (D) uninucleate meiotic embryo sac (ES) with the remnants of degenerating, non-functional megaspores (MS); (E) mature seven-celled Polygonum type embryo sac with an egg cell (EC), two synergids (SY), and a central cell with two polar nuclei (PN) (A,C,E – Naumova et al., 2001; B,D – Osadtchiy et al., 2017).

FIGURE 3

Apomeiotic megasporogenesis in B. holboellii s. l. (A) megaspore mother cell (MMC); (B) diplosporous dyad (Dy); (C) uninucleate diplosporous embryo sac (DES) with remnants of the “megaspore” (“MS”); (D) callose in the cell wall of a diplosporous dyad (B,C – Naumova et al., 2001; A,D – Osadtchiy et al., 2017).

FIGURE 4

Meiosis and apomeiosis in B. holboellii s. l. (A–C,A^∗–C^∗) and B. stricta (D,D^∗). (A,A^∗) metaphase I meiotic spindle (S); (B,B^∗) two metaphase II meiotic spindles (S1 and S2); (C,C^∗) equational division spindle during apomeiosis (S); (D,D^∗) metaphase I meiotic spindle (S) in sexual B. stricta (B) (Osadtchiy et al., 2017).

FIGURE 5

The B. divaricarpa genome is extremely heterozygous. Distribution of the number of 19-mer occurrences in B. stricta, which has only one peak, indicating a highly homozygous genome, and B. divaricarpa, which has 2 peaks with a pronounced difference in height. Note that the number of occurrences of different K-mers in the first peak (ca. 90) is half of that in the second peak (ca. 180), suggesting that first and second peak represent the heterozygous and homozygous part of the genome, respectively. N50 values are based on the assembly of Illumina paired-end reads (100× coverage) by Platanus. Heterozygosity has an immediate effect on the contiguity of the genome assembly.

FIGURE 6

K-mer (27) profiles of genomic sequence reads (Illumina) from apomictic (red) and sexual (blue) B. spatifolia. Note characteristic shape of the right slope on the graphs in all apomictic accessions.

FIGURE 7

Replicating the analysis of B. spatioflia genetic structure variation (Lovell et al., 2017). Sequencing reads from 16 re-sequenced individuals (8 apomict-sexual sympatric pairs) were used to generate a minimum spanning network where edge length is proportional to Mash distance, which estimates the mutation rate between genomic sequences of B. spatiofolia individuals directly from their MinHash sketches (Ondov et al., 2016). Nodes represent sexual (blue) and apomictic (red) individuals.