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

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.

Genetic Variation and Sequence Diversity of Starch Biosynthesis and Sucrose Metabolism Genes in Sweet Potato

“…In this study, we detected genetic variations in 20 genes. It should be mentioned that there might be approximate six copies of each gene in the allohexaploid (B1B1B2B2B2B2) sweet potato genomes [31,58], and our results also showed 1-37 potential homologs or paralogs of each studied gene in the genome database. During the formation and evolution of polyploid genomes, the duplicated genes might exhibit expressional, regulatory or functional divergence [53,59].…”

Haplotype-based phylogenetic analysis uncovers the tetraploid progenitor of sweet potato

“…Gao et al 14 , based on Waxy (Wx) intron sequence variation, suggested that sweet potato arose via hybridization between I. tenuissima and I. littoralis. Subsequently, Gao, et al 15 postulated that the hexaploid sweet potato may be neither a true autopolyploid nor a genuine allopolyploid based on the analysis of 811 conserved single-copy genes. Recently, Yang et al 5 analyzed the phased genome of sweet potato and proposed that sweet potato might have resulted from a cross between a diploid and a tetraploid progenitor.…”

The Expression of IbMYB1 Is Essential to Maintain the Purple Color of Leaf and Storage Root in Sweet Potato [Ipomoea batatas (L.) Lam]

“…Sweet potato is a highly heterozygous crop with 90 chromosomes (2 n = 6 x = 90), and its ploidy type has not yet been clearly determined ( Yang et al, 2017 ; Wu et al, 2018 ; Gao et al, 2020 ). The hexaploidy, high heterozygosity, huge genome, and outcrossing nature make it difficult to analyze the genetics of multiple-copy genes.…”