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.
Highlights
Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh largest crop by global production (FAOSTAT, 2017 data), and an important source of food, feed and industrial raw materials worldwide
Initial comparative analyses of Conserved Ortholog Set II (COSII) cDNAs from I. littoralis, I. tenuissima and I. trifida revealed two distinct lineages between cDNA variants of many COSII genes in I. littoralis, one extremely trifida or tenuissima-like and the other littoralis-specific, which seemed to be more consistent with them being expressed from two homoeologous loci in two diploid subgenomes than from paralogous ones in a diploid genome
The long-lasting disagreement on an auto- versus allohexaploid sweetpotato was rooted in two lines of phylogenetic signals or data that were not consistent with either one of the two mutually exclusive polyploidy types
Summary
Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh largest crop by global production (FAOSTAT, 2017 data), and an important source of food, feed and industrial raw materials worldwide. Nishiyama [6, 7] proposed an “autohexaploid” sweetpotato origin from a hexaploid “I. trifida” This inference seemed to be supported by the morphological and physiological resemblances between sweetpotato and a synthetic hexaploid generated from hybridization of a diploid (K221, B1B1genome) and a tetraploid (K222, B2B2 B2B2 genome) forms of I. trifida (H.B.K.) G. Other analyses of different sets of samples employing some other markers, including those using RFLP [18], RAPD [19], the single-copy β-amylase gene [20] and three types of sweetpotato Waxy intron 2 variants [21], seemed to favor an allohexaploid genome that were more closely related to those of I. trifida, and some other relatives, I. tabascana J.A. McDonald & D.F. Austin, I. littoralis Blume and I. tenuissima Choisy
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call