The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene

Abstract

Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China which has become an emerging economic crop with rapid development. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (LSC, 83,981 bp), and a small single-copy region (SSC, 18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased towards A/T bases. 32 SSRs were distributed in the non-coding regions. Comparative analysis of the chloroplast genome sequence of Jerusalem artichoke and other species of the composite family revealed the chloroplast genome sequences of plants of the composite family to be highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. Phylogenetic analysis showed Helianthus petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution and has the potential to be used as a phylogenetic reconstruction locus in the composite family. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family, and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.

A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences

“…In addition, Watsonia longifolia and Gladiolus communis exhibited significant inversions from petN to trnE-UUC (approximately 3 kb) (Figure 2). In many studies, ycf2 gene alone provides well-supported phylogeny because of its large size and extensive sequence variation (containing many INDELS) uniquely shared by some species and is frequently employed in phylogenetic research on angiosperms (Huang et al, 2010;Zhong et al, 2019;Tang et al, 2022). Our findings revealed significant deletions and inconsistent variations in the ycf2 gene region.…”

“…Members of the Crocoideae, Nivenioideae, and Aristeoideae subfamilies shared a 237-bp deletion in the ycf2 gene (Supplementary Figure S1) as we moved from the basal (Isophysioideae) to the higher clade (Crocoideae, Nivenioideae, and Aristeoideae) (Figure 6). Zhong et al (2019) performed selective locus detection of the ycf2 gene in eight species of the composite family and reported that the ycf2 gene has undergone adaptive evolution. Hu et al (2015); Fan et al (2018); Zhong et al (2019), andWu et al (2020) investigated the positive selection of the protein-coding ycf2 gene and reported its role in adaptation to diverse ecosystems.…”

“…Zhong et al (2019) performed selective locus detection of the ycf2 gene in eight species of the composite family and reported that the ycf2 gene has undergone adaptive evolution. Hu et al (2015); Fan et al (2018); Zhong et al (2019), andWu et al (2020) investigated the positive selection of the protein-coding ycf2 gene and reported its role in adaptation to diverse ecosystems. In our study, the gene ycf2 was to a selective pressure test using a sequence alignment of ycf2 gene that codes for protein to estimate the K a /K s ratio, and the results showed K a /K s >1, indicating positive selection (Supplementary Table S4-4.1).…”

Complete Chloroplast Genome of Shorea macrophylla (Engkabang): Structural Features, Comparative and Phylogenetic Analysis

“…The ycf2, psbI-trnG, ndhA-ndhI, psbZ-trnG, rps12-ndhB, rpl33-rpoA, rpoA-psbB and rpoC1 regions were revealed as mutational hotspots of six Shorea species with two Parashorea species in this study. Among the mutational hotspot region, ycf2, psbI-trnG, psbZ-trnG has been found to have the highest degree of differentiation and hence can be utilised to investigate adaptive evolution traits of the gene [33][34][35][36].…”

Analysis of Six Chloroplast Genomes Provides Insight into the Evolution of Chrysosplenium (Saxifragaceae)

“…ycf2 has become a useful gene for assessing sequence variation and evolution in plants [40]. Positive selection of ycf2 was also found to be involved in adaptation in other species [41]. However, due to the extremely high Ka/Ks value ( =231.51421) and unknown function, ycf2 is a valuable resource for future research of the adaptive evolution of Chrysosplenium.…”