Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato (Ipomoea batatas)

Abstract

As a major plant-specific transcription factor family, SPL genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on SPL genes in the genus Ipomoea are lacking. Here, we identified a total of 29, 27, 26, and 23 SPLs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the Ipomoea SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the Ipomoea lineage-specific whole-genome triplication event, was speculated to have a predominant role in Ipomoea SPL expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in Ipomoea, rice, Arabidopsis, and tomato. These findings support the expansion of SPLs in Ipomoea genus, with most of the SPLs being evolutionarily conserved. Of the 105 Ipomoea SPLs, 69 were predicted to be the targets of miR156, with seven IbSPLs being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues, IbSPLs showed diverse expression patterns, including seven highly expressed IbSPLs in the underground tissues. Furthermore, the expression of 11 IbSPLs was validated using qRT-PCR, and two (IbSPL17/IbSPL28) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six IbSPLs were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four IbSPLs (IbSPL16/IbSPL17/IbSPL21/IbSPL28) clusters with genes involved in “regulation of root morphogenesis,” “cell division,” “cytoskeleton organization,” and “plant-type cell wall organization or biogenesis,” indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the SPLs in the genus Ipomoea but also lays a foundation for further elucidation of the potential functional roles of IbSPLs on storage root development.

Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in four Ipomoea species

“…Therefore, the two recent WGD in I. batatas might be the reason for the discrepancies in the rate of segmental and tandem duplication. The dominance of segmental duplication in the gene family expanding in Ipomoea species had been reported in a previous study; it was found that segmental duplication was speculated to have a predominant role in Ipomoea SQUAMOSA promoter-binding protein-like genes (SPL) expansion; tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c ( Sun et al, 2022 ). Segmental and tandem duplication, along with gene losses, might bring out the uneven distributions of NBS-encoding genes in the four Ipomoea species ( Zhou et al, 2020 ).…”

“…The NBS-encoding gene family has been studied in various species, including Arabidopsis ( Meyers et al, 2003 ), Oryza sativa ( Zhou et al, 2004 ), Zea mays ( Cheng et al, 2012 ), Triticum urartu ( Liu et al, 2017 ), Gossypium hirsutum ( Shi et al, 2018 ), Lagenaria siceraria ( Wang et al, 2022 ), and Cucumis sativus ( Wang et al, 2022 ). The Ipomoea , with great value in the fields of industry and agriculture, is the largest genus in Convolvulaceae ( Austin and Huáman, 1996 ; Liu, 2017 ; Morita and Hoshino, 2018 ; Sun et al, 2022 ). Sweet potato, together with its wild diploid ancestors ( I. trifida and I. triloba ), and its general rootstock ( I. nil ), are all sequenced Ipomoea species ( Hoshino et al, 2016 ; Yang et al, 2017 ; Wu et al, 2018 ).…”

“…Ipomoea is the largest genus of Convolvulaceae and contains 600–700 species ( Austin and Huáman, 1996 ). Ipomoea species are globally distributed with agricultural and industrial importance ( Liu, 2017 ; Morita and Hoshino, 2018 ; Sun et al, 2022 ). Sweet potato, Ipomoea batatas (L.) Lam.…”

Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses

“…The RNA-seq data of ItbPIFs and ItfPIFs in I. triloba and I. trifida were downloaded from the Sweetpotato Genomics Resource ( ; accessed on 10 December 2022) [ 53 ]. The RNA-seq data of IbPIFs in Yan252 and Xuzi3 were obtained from related research [ 96 ]. The expression levels of PIFs were calculated as fragments per kilobase of exon per million fragments mapped (FPKM).…”

Comparative Analysis of Salt Responsive MicroRNAs in Two Sweetpotato [Ipomoea batatas (L.) Lam.] Cultivars With Different Salt Stress Resistance

“…has an indispensable role in reducing poverty and promoting food safety ( Wan et al, 2020 ; Zhang et al, 2020 ; Li et al, 2022 ). Sweetpotato has significant nutritional value for humans, because it contains a variety of nutrients, including protein, anthocyanins, minerals, carotenoids, dietary fiber and vitamins ( Zhu et al, 2020 ; Sun H. et al, 2022 ). However, salt stress has great adverse effects on the growth, fresh weight, health-promoting compounds and antioxidant activity of sweetpotato.…”