The unusual occurrence and developmental diversity of asexual eukaryotes still remain a puzzle. Despite asexual organisms have a theorized two-fold reproductive advantage over sexuals, asexual lineages are rare among multicellular eukaryotes. Justification of such disparity relies on the consequences of a lack of meiosis, which restricts genotype diversity and adaptation to novel conditions while accelerating the genetic degeneration that drives asexual lineages to an early demise. However, evidence indicates asexuals use different strategies to limit negative consequences of ameiosis, and age estimates show some asexual vertebrates and plants are much older than expected. If rapid extinction is not a factor influencing asexuals lifespan, then why asexuals are not more frequent? Here we review traditional ideas and new data and provide a novel unified evolutionary frame to understand the intriguing nature, developmental diversity and maintenance of asexual lineages. As a rule, de novo formation of a functioning asexual genome requires a unique assemblage combining particular sets of genes or gene states to disrupt cellular mechanisms of meiosis and gametogenesis, and affect discrete components of sexuality to produce clonal or hemiclonal offspring. We highlight two usually overlooked but essential conditions to understand the molecular nature of clonal organisms, i.e. a non-recombinant genomic assemblage retaining modifiers of the sexual program, and a complementation between altered reproductive components. These subtle conditions are the basis for physiologically viable and genetically balanced transitions between generations. Genomic and developmental evidence from asexual animals and plants indicates the lack of complementation of molecular changes in the sexual reproductive program is likely the main cause of asexuals' rarity, and can provide an explanatory frame for the developmental diversity and lability of developmental patterns in some asexuals as well as for the discordant time to extinction estimations.

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of the apomictic species Boechera divaricarpa. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. 27048 protein-coding genes were predicted using a hybrid approach that combines homology-based and de novo methods. Also repeats, tRNA and rRNA genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. Also, a detailed analysis of evolution of the APOLLO apomixis-associated locus was performed. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species such as B. divaricarpa.

Zanthoxylum armatum is an forest tree with apomixis characteristic, and RWP-RKs are plant-specific transcription factors known to regulate nitrogen response and embryonic development. However, the genome-wide analysis of RWP-RK family genes in Z.armatum is unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z.armatum, among which 15 genes were belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed close phylogenetic relationship between Z.armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of embryonic development of Z.armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z.armatum.

The hybrid seeds of several important crops with supreme qualities, including yield, biotic and abiotic stress tolerance, have been cultivated from decades. Thus far, a major challenge with hybrid seed, it does not hold ability to produce plants with same qualities over subsequent generations. Apomixis exist naturally an asexual mode of reproduction in flowering plants via avoiding meiosis and ultimately leads to seed production. Apomixis possess potential to preserve hybrid vigor for multiple generations for economically important plant genotypes. The evolution and genetics of asexual seed production is unclear and need much more efforts to find its genetic architecture. To fix hybrid vigor synthetic apomixis has been suggested an alternative. The development of MiMe (Mitosis instead of Meiosis) genotypes are utilized further for clonal gametes production. However, the identification and parental origin of genes responsible for synthetic apomixis are less known and need further understanding. Genome modifications utilizing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (cas9) a reverse genetics tool has paved way to utilize emerging technologies in plant molecular biology. From the last decade, several genes in important crops have been successfully edited. The vast availability of GETs has made the functional genomics studies easy to conduct in crops important for food security. The disruption of expression of genes specific to egg cell MATRILINEAL (MTL) or BABY BOOM1 (BBM1) through CRISPR/Cas genome editing system can promote haploid plants. The establishment of synthetic apomixis by engineering MiMe genotype by genome editing BBM1 expression or disruption of MTL leads toward clonal seed production. In present review, we discussed the current development in plants by utilizing CRISPR/Cas9 technology and its possibility of promoting apomixis in crops to preserve hybrid vigour. In addition to this, genetics, evolution, epigenetic modifications and strategy for MiMe genotype development has been discussed in detail.

Apomictic plants (reproducing via asexual seeds), unlike sexual individuals, avoid meiosis and egg cell fertilization. Consequently, apomixis is very important for fixing maternal genotypes in the next plant generations. Despite the progress in the study of apomixis, molecular and genetic regulation of the latter remains poorly understood. So far APOLLO (Aspartate Glutamate Aspartate Aspartate histidine exonuclease) is one of the very few described genes associated with apomixis in Boechera species. The centromere-specific histone H3 variant encoded by CENH3 gene is essential for cell division. Mutations in CENH3 disrupt chromosome segregation during mitosis and meiosis since the attachment of spindle microtubules to a mutated form of the CENH3 histone fails. This paper presents in silico characteristic of APOLLO and CENH3 genes, which may affect apomixis. Also, we characterize the structure of CENH3, study expression levels of APOLLO and CENH3 in gynoecium/siliques of the natural diploid apomictic and sexual Boechera species at the stages of before and after fertilization. While CENH3 was a single copy gene in all Boechera species, the APOLLO gene have several polymorphic alleles associated with sexual and apomictic reproduction in the Boechera genera. Expression of the APOLLO apo-allele during meiosis was upregulated in gynoecium of apomict B. divaricarpa downregulating after meiosis until 4th day after pollination (DAP). On the 5th DAP, expression in apomictic siliques increased again. In sexual B. stricta gynoecium and siliques APOLLO apo-allele did not express. Expression of the APOLLO sex-allele during and after meiosis in gynoecium of sexual plants was several times higher than that in apomictic gynoecium. However, after pollination the sex-allele was downregulated in sexual siliques to the level of apomicts and increased sharply on the 5th DAP, while in apomictic siliques it almost did not express. At the meiotic stage, the expression level of CENH3 in the gynoecium of apomicts was two times lower than that of the sexual Boechera, decreasing in both species after meiosis and keep remaining very low in siliques of both species for several days after artificial pollination until the 4th DAP, when the expression level raised in sexual B. stricta siliques exceeding 5 times the level in apomictic B. divaricarpa siliques. We also discuss polymorphism and phylogeny of the APOLLO and CENH3 genes.