Phylogeny of <i>PolA1</i> Gene Consistent with the Relationships of U’s Triangle in <i>Brassica</i>

Abstract

The Brassica genus comprises various important species, of which three diploid species, B. rapa (A genome), B. nigra (B), and B. oleracea (C), yielded three different pair-wise amphidiploids: B. juncea (AB), B. napus (AC), and B. carinata (BC), showing the "triangle of U". Although DNA sequences of many genes have been analyzed to reveal the relationships between A, B, and C genomes, the phylogeny of any single-copy nuclear gene has not supported the entire relationships of U's triangle. Most nuclear genomic sequences of plants have genetically recombined between alleles in inter-specific hybrids, while we recently found that intron 19 and nucleotide tag (Ntag) sequences of the single-copy nuclear PolA1 gene, encoding RNA polymerase I's largest subunit, had rarely recombined during the introgressive hybridizations in Aegilops speltoides. Because phylogenetic analysis including recombined sequences cannot reveal the phylogeny before the recombination occurred, only analysis of non-recombinational DNA sequences can resolve the true evolutionary route. In this study, the phylogenetic relationships of the PolA1 gene in the six Brassica species were clearly consistent with U's triangle. In addition, two groups of B. napus were shown divergently to have originated from the amphidiploidization between B. oleracea and two progenitors of B. rapa.

A large deletion within intron 20 sequence of single-copy <i>PolA1</i> gene as a useful marker for the speciation in <i>Oryza</i> AA-genome species

“…japonica 'Nipponbare' (LOC_Os06g40950 and The Rice Annotation Project Database: Os06g0612200 in Rice Genome Annotation Project, Kawahara et al 2013). Recently, particular DNA sequences from exons 19 to 21 of PolA1 gene have been useful to elucidate the phylogenetic relationships of Petunia (Zhang et al 2008), Oryza (Takahashi et al 2009), Triticum (Takahashi et al 2010), Brassica (Fareed et al 2016) and Triticum-Aegilops (Nakamura et al 2009), and Triticum-Aegilops and Hordeum (Rai et al 2012).…”

Triploid Wild Rice (BKK) Strain Found in Bangkok Originated from Hybridizations among Three Parental &lt;i&gt;Oryza&lt;/i&gt; Species

“…15 kb) contains 21 exons on chromosome 6 of rice genome [6]. Phylogenetic studies for the intron 19 and exon 20 sequences of PolA1 gene were useful to analyze relationships in Petunia [7], Aegilops [8], Oryza [2], Triticum-Aegilops [9], Triticum-Hordeum [10], and Brassica [11] [12].…”

“…400 aa) showed a species-specific variation, encoded by exons 19 -21 of PolA1 gene in land plants [13]. The Ptag sequence is useful to classify species in Triticum-Hordeum [10], Brassica [12], and Trichophyton fungi [14]. Therefore, Ptag sequences of BKK strain were determined to reveal species, which were involved in the origin of BKK strain.…”

Oryza Longistaminata-like Cryptic Species Found in the Mekong Delta Probably Involved in the Origin of O. Rufipogon Indica Ancestor

“…Phylogenetic studies for the intron 19 and exon 20 sequences of PolA1 gene were useful to analyze relationships in Petunia (Zhang et al 2008), Aegilops (Nakamura et al 2009), Oryza (Takahashi et al 2009), Triticum-Aegilops (Takahashi et al 2010), Triticum-Hordeum (Rai et al 2012, and Brassica (Fareed et al 2015(Fareed et al , 2016.…”

“…400 aa) showed a speciesspeci c variation, encoded by exons 19 -21 of PolA1 gene in land plants. The Ptag sequence is useful to classify species in Triticum-Hordeum (Rai et al, 2012), Brassica (Fareed et al 2016), and Trichophyton fungi (Yamanishi et al 2017). Therefore, Ptag sequence was determined in order to discriminate specieslevel differences of wild rice strains found in the Mekong Delta.…”