Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)

Genomic survey and expression analysis of cellulose synthase superfamily and COBRA-like gene family in Zanthoxylum bungeanum stipule thorns

The Cellulose Synthase gene (CS) superfamily and COBRA-like (COBL) gene family are essential for synthesizing cellulose and hemicellulose, which play a crucial role in cell wall biosynthesis and the hardening of plant tissues. Our study identified 126 ZbCS and 31 ZbCOBL genes from the Zanthoxylum bungeanum (Zb) genome. Phylogenetic analysis and conservative domain analysis unfolded that ZbCS and ZbCOBL genes were divided into seven and two subfamilies, respectively. Gene duplication data suggested that more than 75% of these genes had tandem and fragment duplications. Codon usage patterns analysis indicated that the ZbCS and ZbCOBL genes prefer ending with A/T base, with weak codon preference. Furthermore, seven key ZbCS and five key ZbCOBL genes were identified based on the content of cellulose and hemicellulose and the expression characteristics of ZbCS and ZbCOBL genes in various stages of stipule thorns. Altogether, these results improve the understanding of CS and COBL genes and provide valuable reference data for cultivating Zb with soft thorns.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01432-x.

Functional Diversification and the Plant Secondary Cell Wall

Much evidence exists suggesting the presence of genetic functional diversification in plants, though literature associated with the role of functional diversification in the evolution of the plant secondary cell wall (SCW) has sparsely been compiled and reviewed in a recent context. This review aims to elucidate, through the examination of gene phylogenies associated with its biosynthesis and maintenance, the role of functional diversification in shaping the critical, dynamic, and characteristic organelle, the secondary cell wall. It will be asserted that gene families resulting from gene duplication and subsequent functional divergence are present and are heavily involved in SCW biosynthesis and maintenance. Furthermore, diversification will be presented as a significant driver behind the evolution of the many functional characteristics of the SCW. The structure and function of the plant cell wall and its constituents will first be explored, followed by a discussion on the phenomenon of gene duplication and the resulting genetic functional divergence that can emerge. Finally, the major constituents of the SCW and their individual relationships with duplication and divergence will be reviewed to the extent of current knowledge on the subject.

Genome-wide analysis of the cellulose toolbox of Primulina eburnea, a calcium-rich vegetable

BACKGROUND

Human-guided crop domestication has lasted for more than 10,000 years. In terms of the domestication and breeding of vegetables, cellulose content in edible tissues is one of the most important traits. Primulina eburnea is a recently developed calcium-rich vegetable with a high soluble and bioavailable calcium content in its leaves. However, the high cellulose content in the leaves hampers the taste, and no research has been reported on the genetic basis of cellulose biosynthesis in this calcium-rich vegetable.

RESULTS

We identified 36 cellulose biosynthesis-involved genes belonging to eight gene families in the P. eburnea genome. The cellulose accumulated decreasingly throughout leaf development. Nineteen genes were considered core genes in cellulose biosynthesis, which were highly expressed in buds but lowly expressed in mature leaves. In the nitrogen fertilization experiment, exogenous nitrogen decreased the cellulose content in the buds. The expressing pattern of 14 genes were consistent with phenotypic variation in the nitrogen fertilization experiment, and thus they were proposed as cellulose toolbox genes.

CONCLUSIONS

The present study provides a strong basis for the subsequent functional research of cellulose biosynthesis-involved genes in P. eburnea, and provides a reference for breeding and/or engineering this calcium-rich vegetable with decreased leaf cellulose content to improve the taste.

Physiological and transcriptomic responses to cold waves of the most cold-tolerant mangrove, Kandelia obovata

Mangrove forests inhabit tropical or subtropical intertidal zones and have remarkable abilities in coastline protection. Kandelia obovata is considered the most cold-tolerant mangrove species and has been widely transplanted to the north subtropical zone of China for ecological restoration. However, the physiological and molecular mechanisms of K. obovata under colder climate was still unclear. Here, we manipulated the typical climate of cold waves in the north subtropical zone with cycles of cold/recovery and analyzed the physiological and transcriptomic responses of seedlings. We found that both physiological traits and gene expression profiles differed between the first and later cold waves, indicating K. obovata seedlings were acclimated by the first cold experience and prepared for latter cold waves. 1,135 cold acclimation-related genes (CARGs) were revealed, related to calcium signaling, cell wall modification, and post-translational modifications of ubiquitination pathways. We identified the roles of CBFs and CBF-independent transcription factors (ZATs and CZF1s) in regulating the expression of CARGs, suggesting both CBF-dependent and CBF- independent pathways functioned in the cold acclimation of K. obovata. Finally, we proposed a molecular mechanism of K. obovata cold acclimation with several key CARGs and transcriptional factors involved. Our experiments reveal strategies of K. obovata coping with cold environments and provide prospects for mangrove rehabilitation and management.

Identification and bioinformatic analysis of the CaCesA/Csls family members and the expression of the CaCslD1 in the flower buds of CMS/Rf system in pepper

The cellulose synthase gene superfamily contains cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, which synthesize cellulose and hemicellulose in plant cell walls and play a crucial role in plant growth and development. However, the CesA/Csl gene family has not been reported in pepper. Therefore, the genome-wide research of the CaCesA/CaCsl gene family was conducted in pepper. In this study, a total of 39 CaCesA/CaCsls genes (10 CesAs genes and 29 Csls genes) were identified in pepper and unevenly distributed on 11 chromosomes. These CaCesA/Csls were divided into seven subfamilies (CesAs, CslAs, CslBs, CslCs, CslDs, CslEs, CslGs), and most of CaCesA/Csls genes are closely related to AtCesA/Csls genes. The cis-acting elements in the promoters of CaCesA/Csls genes are mainly related to hormone response and stress response. There are ten collinear gene pairs between the CesA/Csls gene family of pepper and Arabidopsis, and four fragment duplication gene pairs of the CaCesA/Csls genes were discovered. RNA-seq analysis shows that the majority of CaCesA/Csls are expressed in a variety of plant tissues, indicating that most CaCesA/Csls gene expression patterns are not organ-specific, and CaCslD1/D4 have the highest expression in anthers, followed by petal, ovary, and F9. RNA-seq analysis shows that most CaCesA/Csls are responsive to five hormones (IAA, GA₃, ABA, SA, and MeJA). The tissue-specific expression analysis of the CaCslD1 gene shows that the CaCslD1 gene is expressed specifically in flowers. In the flower buds IV of cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system, CaCslD1 reach the highest expression respectively. However, the relative expression level of CaCslD1 in the fertile accessions is extremely significantly higher than in the sterile accessions. This study shows an overall understanding of the CaCesA/Csls gene family and provides a new insight for understanding the function of CaCslD1 in pollen development and exploring the fertility restoration of CMS in pepper.

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.

The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton

Cellulose synthases (CesAs) are multi-subunit enzymes found on the plasma membrane of plant cells and play a pivotal role in cellulose production. The cotton fiber is mainly composed of cellulose, and the genetic relationships between CesA genes and cotton fiber yield and quality are not fully understood. Through a phylogenetic analysis, the CesA gene family in diploid Gossypium arboreum and Gossypium raimondii, as well as tetraploid Gossypium hirsutum ('TM-1') and Gossypium barbadense ('Hai-7124' and '3-79'), was divided into 6 groups and 15 sub-groups, with each group containing two to five homologous genes. Most CesA genes in the four species are highly collinear. Among the five cotton genomes, 440 and 1929 single nucleotide polymorphisms (SNPs) in the CesA gene family were identified in exons and introns, respectively, including 174 SNPs resulting in amino acid changes. In total, 484 homeologous SNPs between the A and D genomes were identified in diploids, while 142 SNPs were detected between the two tetraploids, with 32 and 82 SNPs existing within G. hirsutum and G. barbadense, respectively. Additionally, 74 quantitative trait loci near 18 GhCesA genes were associated with fiber quality. One to four GhCesA genes were differentially expressed (DE) in ovules at 0 and 3 days post anthesis (DPA) between two backcross inbred lines having different fiber lengths, but no DE genes were identified between these lines in developing fibers at 10 DPA. Twenty-seven SNPs in above DE CesA genes were detected among seven cotton lines, including one SNP in Ghi_A08G03061 that was detected in four G. hirsutum genotypes. This study provides the first comprehensive characterization of the cotton CesA gene family, which may play important roles in determining cotton fiber quality.

Genome-Wide Identification of Banana Csl Gene Family and Their Different Responses to Low Temperature between Chilling-Sensitive and Tolerant Cultivars

The cell wall plays an important role in responses to various stresses. The cellulose synthase-like gene (Csl) family has been reported to be involved in the biosynthesis of the hemicellulose backbone. However, little information is available on their involvement in plant tolerance to low-temperature (LT) stress. In this study, a total of 42 Csls were identified in Musa acuminata and clustered into six subfamilies (CslA, CslC, CslD, CslE, CslG, and CslH) according to phylogenetic relationships. The genomic features of MaCsl genes were characterized to identify gene structures, conserved motifs and the distribution among chromosomes. A phylogenetic tree was constructed to show the diversity in these genes. Different changes in hemicellulose content between chilling-tolerant and chilling-sensitive banana cultivars under LT were observed, suggesting that certain types of hemicellulose are involved in LT stress tolerance in banana. Thus, the expression patterns of MaCsl genes in both cultivars after LT treatment were investigated by RNA sequencing (RNA-Seq) technique followed by quantitative real-time PCR (qPCR) validation. The results indicated that MaCslA4/12, MaCslD4 and MaCslE2 are promising candidates determining the chilling tolerance of banana. Our results provide the first genome-wide characterization of the MaCsls in banana, and open the door for further functional studies.