The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat

Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107 309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.DATA AVAILABILITY: The data supporting the findings of this work are available within the paper and its Supporting Information files. The data sets generated and analyzed during this study are available from the corresponding author upon request. All the whole-genome raw data generated during this study have been deposited in the SRA database under BioProject number PRJNA759075. Transcriptome clean data have been deposited in the SRA database under BioProject number PRJNA759717. The final chromosome-scale genome assembly and annotation data have been deposited in the Figshare database (https://doi.org/10.6084/m9.figshare.19142558.v1).Six Talent Peaks Project of Jiangsu Province (NY-042); Open Fund of the Jiangsu Key Laboratory for the Research and Utilization of Plant Resources (JSPKLB201928); Talent Training Funds of the Institute of Botany, Jiangsu Province and Chinese Academy of Sciences.https://academic.oup.com/hrBiochemistryGeneticsMicrobiology and Plant Patholog

Genome-Wide Identification and Analysis of <i>MYB</i> Transcription Factor Family in <i>Hibiscus hamabo</i>

MYB transcription factors constitute one of the largest gene families in plants and play essential roles in the regulation of plant growth, responses to stress, and a wide variety of physiological and biochemical processes. In this study, 204 MYB proteins (HhMYBs) were identified in the Hibiscus hamabo Sieb. et Zucc (H. hamabo) genome and systematically analyzed based on their genomic sequence and transcriptomic data. The candidate HhMYB proteins and MYBs of Arabidopsis thaliana were divided into 28 subfamilies based on the analysis of their phylogenetic relationships and their motif patterns. Expression analysis using RNA-seq and quantitative real-time PCR (qRT-PCR) indicated that most HhMYBs are differentially regulated under drought and salt stresses. qRT-PCR analysis of seven selected HhMYBs suggested that the HhMYB family may have regulatory roles in the responses to stress and hormones. This study provides a framework for a more comprehensive analysis of the role of MYBs in the response to abiotic stress in H. hamabo

Complete chloroplast genome sequence of Kosteletzkya pentacarpos

Kosteletzkya pentacarpos is a promising plant being developed as a salt-tolerant biofuel crop that also the ability to fix heavy metals. Here, high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of K. pentacarpos. The full length of the chloroplast genome is 161,777 bp, comprising a large single-copy region of 90,019 bp, a small single-copy region of 18,978 bp, and a pair of inverted repeats of 26,390 bp. A total of 113 genes were annotated, including 79 protein-coding, 30 transfer RNA, and 4 ribosomal RNA genes. Phylogenetic analysis based on whole chloroplast genome sequences showed that K. pentacarpos has a close relationship with Abelmoschus in Malvaceae. This study increases the available genomic information on K. pentacarpos, and provides a basis for the rational exploitation and utilization of germplasm resources

The complete chloroplast genome sequence of Hibiscus coccineus

Hibiscus coccineus is famous for its wide geographical distribution and the showy flowers of scarlet rose mallow. It belongs to the Malvaceae family and has greatly ornamental and ecological value. In this study, high-throughput sequencing and bioinformatics technology were used to assemble the complete chloroplast genome sequence, which will provide more genomic information for studying the genetic diversity and phylogenetic relationship. The full length of chloroplast genome is 160,280 bp, composed of a large single-copy (LSC) region of 89,121 bp, a small single-copy (SSC) region of 18,673 bp, and two inverted repeats (IRs) of 26,243 bp. A total of 113 genes were annotated, including 79 protein-coding genes, 30 tRNA, and four rRNA genes. Phylogenetic tree analysis revealed that the Hibiscus coccineus is closest to Hibiscus mutabilis in the Hibiscus L

<i>IlAP2</i>, an AP2/ERF Superfamily Gene, Mediates Cadmium Tolerance by Interacting with <i>IlMT2a</i> in <i>Iris lactea</i> var. <i>chinensis</i>

Cadmium (Cd) stress has a major impact on ecosystems, so it is important to find suitable Cd-tolerant plants while elucidating the responsible molecular mechanism for phytoremediation to manage Cd soil contamination. Iris lactea var. chinensis is an ornamental perennial groundcover plant with strong tolerance to Cd. Previous studies found that IlAP2, an AP2/ERF superfamily gene, may be an interacting partner of the metallothionein gene IlMT2a, which plays a key role in Cd tolerance. To study the role of IlAP2 in regulating Cd tolerance in I. lactea, we analyzed its regulation function and mechanism based on a yeast two-hybrid assay, a bimolecular fluorescence complementation test, quantitative real-time PCR, transgenics and transcriptome sequencing. The results showed that IlAP2 interacts with IlMT2a and may cooperate with other transcription factors to regulate genes involved in signal transduction and plant hormones, leading to reduced Cd toxicity by hindering Cd transport. These findings provide insights into the mechanism of IlAP2-mediated stress responses to Cd and important gene resources for improving plant stress tolerance in phytoremediation

Transcriptome Profiling of Louisiana iris Root and Identification of Genes Involved in Lead-Stress Response

Louisiana iris is tolerant to and accumulates the heavy metal lead (Pb). However, there is limited knowledge of the molecular mechanisms behind this feature. We describe the transcriptome of Louisiana iris using Illumina sequencing technology. The root transcriptome of Louisiana iris under control and Pb-stress conditions was sequenced. Overall, 525,498 transcripts representing 313,958 unigenes were assembled using the clean raw reads. Among them, 43,015 unigenes were annotated and their functions classified using the euKaryotic Orthologous Groups (KOG) database. They were divided into 25 molecular families. In the Gene Ontology (GO) database, 50,174 unigenes were categorized into three GO trees (molecular function, cellular component and biological process). After analysis of differentially expressed genes, some Pb-stress-related genes were selected, including biosynthesis genes of chelating compounds, metal transporters, transcription factors and antioxidant-related genes. This study not only lays a foundation for further studies on differential genes under Pb stress, but also facilitates the molecular breeding of Louisiana iris

Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc

The basic helix-loop-helix (bHLH) family of transcription factors is one of the most significant and biggest in plants. It is involved in the regulation of both growth and development, as well as stress response. Numerous members of the bHLH family have been found and characterized in woody plants in recent years. However, no systematic study of the bHLH gene family has been published for Hibiscus hamabo Sieb. et Zucc. In this research, we identified 162 bHLH proteins (HhbHLHs) from the genomic and transcriptomic datasets of H. hamabo, which were phylogenetically divided into 19 subfamilies. According to a gene structural study, the number of exon-introns in HhbHLHs varied between zero and seventeen. MEME research revealed that the majority of HhbHLH proteins contained three conserved motifs, 1, 4, and 5. The examination of promoter cis-elements revealed that the majority of HhbHLH genes had several cis-elements involved in plant growth and development and abiotic stress responses. In addition, the overexpression of HhbHLH2 increased salt and drought stress tolerance in Arabidopsis

Transcriptome Analysis Reveals Regulatory Framework for Salt and Drought Tolerance in Hibiscus hamabo Siebold &amp; Zuccarini

Hibiscus hamabo Siebold &amp; Zuccarini (H. hamabo) is tolerant to salt and drought conditions, but the molecular mechanisms that underlie this stress tolerance remain unclear. In this study, the transcriptome of H. hamabo roots was investigated under NaCl or PEG treatment. A total of 20,513 and 27,516 significantly changed known genes at 6 h and 24 h, respectively, were detected between the salt or drought treatments and the control libraries. Among these, there were 3845 and 7430 overlapping genes under the two stresses at 6 h and 24 h, respectively. Based on the analysis of enriched KEGG pathways and clustering of expression patterns, the DEGs that were continuously up- or down-regulated under both salt and drought treatments were mainly enriched in MAPK signaling pathway, transcription factors, transporters and other pathways. The transcriptome expression profiles of H. hamabo provide a genetic resource for identifying common regulatory factors involved in responses to different abiotic stresses. In addition, the identified factors may be useful to developing genetic breeding strategies for the Malvaceae

Erratum Xu T. et al. Cloning and Expression Analysis of MEP Pathway Enzyme-encoding Genes in Osmanthus fragrans. Genes 2016, 7, 78

The authors wish to make the following correction to their paper [...