Hexaploid sweetpotato (Ipomoea batatas (L.) Lam.) may not be a true type to either auto- or allopolyploid.

Gao M, Soriano SF, Cao Q, Yang X, Lu G.

PLoS One. 2020 Mar 3;15(3):e0229624. doi: 10.1371/journal.pone.0229624. eCollection 2020.

Abstract

To better define the sweetpotato polyploidy, we sought to reconstruct phylogenies of its subgenomes based on hybridization networks that could trace reticulate lineages of differentiated homoeolog triplets of multiple single-copy genes. In search of such homoeolog triplets, we distinguished cDNA variants of 811 single-copy Conserved Ortholog Set II (COSII) genes from two sweetpotato clones into variation partitions specified by corresponding homologs from two I. trifida lines, I. tenuissima and I. littoralis using a phylogenetic partition method, and amplicon variants of the COSII-marker regions from 729 of these genes from two sweetpotato clones into putative homoeoallele groups using haplotype tree and the partition methods referenced by corresponding homologs from I. tenuissima. These analyses revealed partly or completely differentiated expressed-homoeologs and homoeologs from a majority of these genes with three important features. 1. Two variation types: the predominant interspecific variations (homoeoalleles), which are non-randomly clustered, differentially interspecifically conserved or sweetpotato-specific, and the minor intraspecific ones (alleles), which are randomly distributed mostly at non-interspecifically variable sites, and usually sweetpotato-specific. 2. A clear differentiation of cDNA variants of many COSII genes into the variation partition specified by I. tenuissima or I. littoralis from that by I. trifida. 3. Three species-homolog-specified and one sweetpotato-specific variation partitions among 293 different COSII cDNAs, and two or three out of the four partitions among cDNA variants of 306 COSII genes. We then constructed hybridization networks from two concatenations of 16 and 4 alignments of 8 homologous COSII cDNA regions each, which included three taxa of expressed homoeologs in a triple-partition combination from the 16 or 4 sweetpotato COSII genes and 5 taxa each of respective cDNA homologs from the three sweetpotato relatives and I. nil, and inferred a species tree embodying both networks. The species tree predicted close-relative origins of three partly differentiated sweetpotato subgenomes.

See https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229624

Figure 2:

Illustration of two distinguishable forms of variations and four phylogenetic partitions among cDNA variants of some COSII genes in sweetpotato.

The two alignments A-1 and B in zoom-out variation-highlighting views were two concatenations (_C1 and _C2) of 16 and 4 alignment blocks, respectively, which included three cDNA variants of the 16 and 4 COSII genes from the sweetpotato SC1149-19 or Tanzania clones (combination of IB_ with_C1 or _C2), and their homologs from I. tenuissima (IT_), I. trifida (Itr_ and Itrk_ for two lines), I. littoralis (IL_) and I. nil (Inil_) in matching column-orders. Black bars highlight all sequence disagreements at various positions against the consensus in individual alignment blocks. The green and maroon triangles indicate sites of two distinguishable forms of variations in among cDNA variants of some COSII genes in sweetpotato. The three cDNA variants each of the 4 and 16 sweetpotato COSII genes carried differential non-random clusters of variations that are either well conserved in one of the reference homologs from I. trifida, I. tenuissima and I. littoralis (as in A), or unshared (_Hp4_ in B) at the common interspecific variable sites, and could be thus distinguished into four species-specified phylogenetic partitions, which were marked with _Itr/Itrk_, _Itn_, _Ils_ and _Hp4_, and shaded with blue, purple, red and pink colors, respectively. The A-2 and A-3 alignments are zoom-in views of the first four concatenated blocks, and the first 132-bp (consensus length) of the fourth block in the first concatenation, respectively. The A-3 alignment also illustrates detailed phylogenetic variation partitions of three cDNA variants of the sweetpotato COSII gene (IB_ and CIP_ for isotigs from the SC1149-19 and Tanzania clones, respectively) with corresponding cDNA homologs from the three relatives.

https://doi.org/10.1371/journal.pone.0229624.g002