An apomixis-linkedORC3-like pseudogene is associated with silencing of its functional homolog in apomicticPaspalum simplex

Abstract

Apomixis in plants consists of asexual reproduction by seeds. Here we characterized at structural and functional levels an apomixis-linked sequence of Paspalum simplex homologous to subunit 3 of the ORIGIN RECOGNITION COMPLEX (ORC3). ORC is a multiprotein complex which controls DNA replication and cell differentiation in eukaryotes. Three PsORC3 copies were identified, each one characterized by a specific expression profile. Of these, PsORC3a, specific for apomictic genotypes, is a pseudogene that was poorly and constitutively expressed in all developmental stages of apomictic flowers, whereas PsORC3b, the putative functional gene in sexual flowers, showed a precise time-related regulation. Sense transcripts of PsORC3 were expressed in the female cell lineage of both apomictic and sexual reproductive phenotypes, and in aposporous initials. Although strong expression was detected in sexual early endosperm, no expression was present in the apomictic endosperm. Antisense PsORC3 transcripts were revealed exclusively in apomictic germ cell lineages. Defective orc3 mutants of rice and Arabidopsis showed normal female gametophytes although the embryo and endosperm were arrested at early phases of development. We hypothesize that PsORC3a is associated with the down-regulation of its functional homolog and with the development of apomictic endosperm which deviates from the canonical 2(maternal):1(paternal) genome ratio.

Evolution of Gene Duplication in Plants

“…The second explanation is that some pseudogenes may still be functional as truncated proteins or as RNA. For example, apomixis in the grass Paspalum simplex is hypothesized to be the consequence of antisense regulation by the transcript of a pseudogene related to the ORIGIN RECOGNITION COMPLEX3 gene (Siena et al, 2016). However, there is no direct evidence that the pseudogene is responsible for the antisense transcript.…”

A reference floral transcriptome of sexual and apomictic Paspalum notatum

“…In all cases, several putative protein-coding regions and a large number of highly repetitive sequences have been detected [30, 39–42]. This approach has recently allowed the identification of a key gene ( BABYBOOM ) related with parthenogenesis in P. squamulatum [43] and an apomixis-linked pseudogene ( PsORC3 -like) associated with the control of endosperm formation in P. simplex [44]. However, the extent of the non-recombinant ACL and its high gene content complicate the identification of the apomixis trigger/s by positional cloning, turning into one of the major drawbacks for the isolation of apomictic determinant/s by direct genetic approaches.…”

Apomixis-related genes identified from a coexpression network inPaspalum notatum, a Neotropical grass

“…Therefore, this mode of reproduction has become the subject of 101 exhaustive cytoembryological, cytogenetic and molecular analyses [10,25]. Some key genes 102 associated with the components of apomixis and the isolation of some sequence candidates have 103 6 already been discovered [6,12,14,[27][28][29][30][31][32][33][34][35][36][37][38][39][40][41]. However, insights into the genetic mechanisms 104 underlying asexual reproduction in natural apomicts are still needed to develop a stable and 105…”

“…universal apomixis system to be applied in breeding programs [39]. Given the complexity of this 106 trait, an understanding of the genomic structure of the apomictic locus is likely to be an essential 107 prerequisite for manipulation of the sexual pathway in model plants or economically important 108 crops [15].…”

“…Since then, several other candidate genes have been reported using P. notatum and P. simplex 384 species [14,27,30,31] and more recently, the first approach using RNA-seq was published for 385 bahiagrass based on expression profiling of apomictic and sexual flowers [40]. Some of these 386 candidate genes had been investigated in more detail [35,[37][38][39]. However, many questions 387 remain unanswered, and further research is needed to define the relationships between the 388 structure, the position, and the function of the known apomixis-linked genes [8].…”