Full-length transcriptome characterization and comparative analysis of Gleditsia sinensis

Xiao, Feng; Zhao, Yang; Wang, Xiurong; Jian, Xueyan

doi:10.1186/s12864-023-09843-y

Cited by 3 publications

(1 citation statement)

References 56 publications

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“…G. velutina is endemic to Hunan Province, China, and is a rare and endangered plant under national key protection 41 . Stress-related genes had been positively selected during the evolution through comparative transcriptome analysis of Gleditsia genus 42 . In this study, positive selection was acting on five genes ( rpoA , rpl20 , atpB , ndhA , ycf4 ), which were identified under positive selection (Ka/Ks > 1), Ka/Ks ratio of most gene were less than 1, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Gleditsia species underwent purifying selection, the purifying selection on most chloroplast genes within Gleditsia would be evolutionary result of the preservation of the adaptive characteristics of Gleditsia species.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Xiao,

Zhao,

Wang

et al. 2024

Sci Rep

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The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8–75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as “rps16-trnQ”, “trnT-trnL”, “ndhG-ndhI”, and "rpl32-trnL” in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.

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Section: Discussionmentioning

confidence: 99%

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Xiao,

Zhao,

Wang

et al. 2024

Sci Rep

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Analysis of differential mRNA and miRNA expression induced by heterogeneous grafting in Gleditsia sinensis

Xiao,

Zhao,

Wang

et al. 2024

International Journal of Biological Macromolecules

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Transcriptome analysis reveals regulatory mechanisms of different drought-tolerant Gleditsia sinensis seedlings under drought stress

Liu,

Zhao,

Wang

et al. 2024

BMC Genom Data

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Background Gleditsia sinensis is a significant tree species from both ecological and economic perspectives. However, its growth is hampered by temporary droughts during the seedling stage, thereby impeding the development of the G. sinensis industry. Drought stress and rehydration of semi-annual potted seedlings using an artificial simulated water control method. RNA sequencing (RNA-seq) analyses were conducted on leaves collected from highly resistant (HR) and highly susceptible (HS) seedling families at five different stages during the process of drought stress and rehydration to investigate their gene expression patterns. Results The differentially expressed genes (DEGs) were predominantly enriched in pathways related to “chloroplast” (GO:0009507), “photosynthesis” (GO:0015979), “plant hormone signal transduction” (map04075), “flavonoid biosynthesis” (map00941), “stress response”, “response to reactive oxygen species (ROS)” (GO:0000302), “signal transduction” (GO:0007165) in G. sinensis HR and HS families exposed to mild and severe drought stress. Additionally, the pathways related to “plant hormone signal transduction” (map04075), and osmoregulation were also enriched. The difference in drought tolerance between the two families of G. sinensis may be associated with “transmembrane transporter activity” (GO:0022857), “stress response”, “hormones and signal transduction” (GO:0007165), “cutin, suberine and wax biosynthesis” (map00073), “ribosome” (map03010), “photosynthesis” (map00195), “sugar metabolism”, and others. An enrichment analysis of DEGs under severe drought stress suggests that the drought tolerance of both families may be related to “water-soluble vitamin metabolic process” (GO:0006767), “photosynthesis” (map00195), “plant hormone signal transduction” (map04075), “starch and sucrose metabolism” (map00500), and “galactose metabolism” (map00052). Osmoregulation-related genes such as delta-1-pyrroline-5-carboxylate synthase (P5CS), Amino acid permease (AAP), Amino acid permease 2 (AAP2) and Trehalose-phosphate synthase (TPS), as well as the antioxidant enzyme L-ascorbate peroxidase 6 (APX6), may be significant genes involved in drought tolerance in G. sinensis. Five genes were selected randomly to validate the RNA-seq results using quantitative real-time PCR (RT-qPCR) and they indicated that the transcriptome data were reliable. Conclusions The study presents information on the molecular regulation of the drought tolerance mechanism in G. sinensis and provides a reference for further research on the molecular mechanisms involved in drought tolerance breeding of G. sinensis.

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Full-length transcriptome characterization and comparative analysis of Gleditsia sinensis

Cited by 3 publications

References 56 publications

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

Analysis of differential mRNA and miRNA expression induced by heterogeneous grafting in Gleditsia sinensis

Transcriptome analysis reveals regulatory mechanisms of different drought-tolerant Gleditsia sinensis seedlings under drought stress

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