Phylogenetic relationships in the genus Avena based on the nuclear pgk1 gene

Abstract

22The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, 23 eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 24 3-phosphoglycerate kinase gene(Pgk1). A significant deletion (131 bp) was detected 25 in all the C genome homoeologues which reconfirmed a major structural divergence 26 between the A and C genomes. Phylogenetic analysis indicated the C p genome is 27 more closely related to the polyploid species than is the C v genome. Two haplotypes 28 of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of 29 the barbata group showed a close relationship with the A s genome diploid species, 30 supporting the hypothesis that both the A and B genomes are derived from an A s 31 genome. Two haplotypes were also detected in A. agadiriana, which showed close 32 relationships with the A s genome diploid and the A c genome diploid, respectively, 33 emphasizing the important role of the A c genome in the evolution of A. agadiriana. 34 Three homoeologues of thePgk1 gene were detected in five hexaploid accessions. 35 The homoeologues that might represent the D genome were tightly clustered with 36 the tetraploids A. marrocana and A. murphyi, but did not show a close relationship 37 with any extant diploid species. 38 42 [5]. The evolutionary history of Avena species has been discussed for decades, and 43 3 remains a matter of debate despite considerable research effort in this field. 44 Cytologically, three ploidy levels are recognized in the genus Avena: diploid, 45 tetraploid, and hexaploid, with a base number of seven chromosomes [6, 7]. The 46 diploids are divided clearly into two distinct lineages with the A and C genomes. All 47 hexaploid species share the same genomic constitution of ACD, corroborated by 48 fertile interspecific crosses among each other, as well as by their similar genome 49 sizes [8]. With less certainty, the tetraploids have been designated as AB or AA, AC or 50 DC, and CC genomes [9]. It is noteworthy that the B and D genomes within the 51 polyploid species have not been identified in any extant diploid species. There are 52 three C genome diploid species, which have been grouped into two genome types 53

Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

“…For subclade I, A. sativa is sister to diploid A. brevis and tetraploid A. murphyi based on the ten most polymorphic coding regions and non-coding regions respectively (Additional file 20 : Figure S8c, S8d). Such variation indicates that A. brevis and A. murphyi might carry a diverged A-genome from the most likely A-genome diploid ancestor, A. longiglumis , supported by nuclear gene Pgk1 too [ 23 ]. It is also evident that the most frequently used chloroplast markers (including trnL-trnF and matK ) show few polymorphisms (0.0058, 0.0037) at the interspecific level with respect to adding outgroup wheat (0.0166, 0.0136).…”

“…If the distribution of plastome repeat sequences can be determined, it is feasible to predict microstructural variations by the correlation analyses between repeats, indels and substitutions. In addition to the paucity of genomic resources, the A-genome lineage phylogeny is enigmatic in Avena [ 19 , 23 , 24 ]. Thus, it is important to fully address polymorphic regions of Avena chloroplasts in an evolutionary context.…”

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

“…On the other hand, pAs120 probe showed weak dispersed signals along all of the 28 chromosomes, thus, the evidence provided here should be taken as putative and encouraging for further exploration of this species. The phylogenetic analysis supported A. agadiriana being closely related to A. canariensis and A. longiglumis (Chew et al, 2016; Peng et al, 2018). Some authors speculated that the genome composition of this species might be AADD due to some similarities to CCDD and AACCDD Avena groups (Badaeva et al, 2010; Luo et al, 2018c), but our FISH signals of A and D genome-specific probes rather indicated an autopolyploid origin of A. agadiriana .…”

“…Species having AABB genomes ( A. barbata, A. vaviloviana, A. abyssinica ) show a close relationship with A. wiestii or A. hirtula . Peng et al (2018) suggested that these species derived through autopolyploidization of As genome, contrary to Badaeva et al (2010) and Irigoyen et al (2001) who proposed allotetraploid origin. According to Peng et al (2018), A. agadiriana, which developed independently, is closely related to the As and A c genomes, but the genome composition of this species remains debatable (this paper; Badaeva et al, 2010; Yan et al, 2016; Luo et al, 2018c).…”

“…Peng et al (2018) suggested that these species derived through autopolyploidization of As genome, contrary to Badaeva et al (2010) and Irigoyen et al (2001) who proposed allotetraploid origin. According to Peng et al (2018), A. agadiriana, which developed independently, is closely related to the As and A c genomes, but the genome composition of this species remains debatable (this paper; Badaeva et al, 2010; Yan et al, 2016; Luo et al, 2018c). Phylogenetic analysis conducted by Peng et al (2018) indicated that C p genome ( A. eriantha, A. clauda ) is more closely related to CCDD-tetraploids and AACCDD-hexaploids than Cv genome ( A. ventricosa ).…”