Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops with high storage roots yield. The formation and expansion rate of storage root (SR) plays a crucial role in the production of sweet potato. Lignin affects the SR formation; however, the molecular mechanisms of lignin in SR development have been lacking. To reveal the problem, we performed transcriptome sequencing of SR harvested at 32, 46, and 67 days after planting (DAP) to analyze two sweet potato lines, Jishu25 and Jishu29, in which SR expansion of Jishu29 was early and had a higher yield. A total of 52,137 transcripts and 21,148 unigenes were obtained after corrected with Hiseq2500 sequencing. Through the comparative analysis, 9577 unigenes were found to be differently expressed in the different stages in two cultivars. In addition, phenotypic analysis of two cultivars, combined with analysis of GO, KEGG, and WGCNA showed the regulation of lignin synthesis and related transcription factors play a crucial role in the early expansion of SR. The four key genes swbp1, swpa7, IbERF061, and IbERF109 were proved as potential candidates for regulating lignin synthesis and SR expansion in sweet potato. The data from this study provides new insights into the molecular mechanisms underlying the impact of lignin synthesis on the formation and expansion of SR in sweet potatoes and proposes several candidate genes that may affect sweet potato yield.

Sweet potato (Ipomoea batatas (L.) Lam.) is an important root crop in China, playing significant roles in ensuring national food security and increasing farmers’ income. The sprouting capability of sweet potato storage roots determines the quality of sweet potato seedlings and serves as a prerequisite for ensuring yield and quality. With the increasing severity of sweet potato viral diseases, the decline of the sprouting capability of seed roots has led to severe declines in both the yield and quality of sweet potatoes. It is urgent to uncover the genetic basis and molecular mechanisms underlying the sprouting capabilities of storage roots with different virus contents. In this study, storage roots with different virus contents of two sweet potato varieties, Jishu 25 (J25) and Jishu 26 (J26), were evaluated for sprouting capability and virus content, including chlorotic stunt virus (CSV), feathery mottled virus (FMV), sweet potato virus G (SPVG), sweet potato latent virus (SPLV), and sweet potato chlorotic fleck virus (SPCFV). The results show that the storage roots with low virus levels of both varieties exhibited stronger sprouting capability and lower virus content. Comparative transcriptome analysis of the differences in sprouting capabilities between storage roots with different virus content revealed that the starch metabolism, cellulose metabolism, jasmonic acid (JA) signaling pathway, and salicylic acid (SA) signaling pathways are potential biological pathways contributing to the differences in sprouting capabilities between storage roots with different virus contents. This study provides evidence for further research on the sprouting mechanisms of sweet potatoes.

Plant evolution started with unicellular algae, gradually evolving multicellularity and terrestrial colonization. These evolutionary events were accompanied by the interplay of chromosome polyploidization, rearrangement, gene loss, and point mutation. We counted the proportion of nucleotide combinations in the genome sequences of 64 sequenced plants, and analyzed the significant difference in these nucleotide combination proportions among algae, monocotyledons and dicotyledons. The correlation of highly significant different and no significant different nucleotide combinations was analyzed respectively. Nucleotide combinations and their reverse complementary sequence proportions were analyzed in different functional regions of the genome. These results reveal that some nucleotide combinations are subject to strict selection, and these combinations have a higher proportion in the CDS regions and lower proportion in the intergenic regions. Meanwhile, there are some nucleotide combinations that are under less selective pressure, and these combinations have a higher proportion in the intergenic regions and lower proportion in the CDS regions. Cluster analysis based on trinucleotide to octanucleotide combination proportions reveals that plant genome evolution is accompanied by clade-wide differentiation of genome-wide nucleotide composition patterns, in addition to well-documented chromosomal polyploidization, structural rearrangement and gene loss events. We analyzed the changes in the proportion of nucleotide combinations at the genome level in 64 sequenced plants, providing a new idea for studying genome evolution in the plant kingdom.