Comparative Transcriptome Analysis Reveals Hormone Signaling Genes Involved in the Launch of Culm-Shape Differentiation in Dendrocalamus sinicus

Mutant IAA21 genes from Dendrocalamus sinicus Chia et J. L. Sun inhibit stem and root growth in transgenic tobacco by interacting with ARF5

Woody bamboos are important resource of industrial fibres. Auxin signaling plays a key role in multiple plant developmental processes, as yet the role of auxin/indole acetic acid (Aux/IAA) in culm development of woody bamboos has not been previously characterized. Dendrocalamus sinicus Chia et J. L. Sun is the largest woody bamboo documented in the world. Here, we identified two alleles of DsIAA21 gene (sIAA21 and bIAA21) from the straight- and bent-culm variants of D. sinicus, respectively, and studied how the domains I, i, and II of DsIAA21 affect the gene transcriptional repression. The results showed that bIAA21 expression was rapidly induced by exogenous auxin in D. sinicus. In transgenic tobacco, sIAA21 and bIAA21 mutated in domains i, and II significantly regulated plant architecture and root development. Stem cross sections revealed that parenchyma cells were smaller in transgenic plants than that in wild type plants. Domain i mutation changed the leucine and proline at position 45 to proline and leucine (siaa21L45P and biaa21P45L) strongly repressed cell expansion and root elongation by reducing the gravitropic response. Substitution of isoleucine with valine in domain II of the full length DsIAA21 resulted in dwarf stature in transgenic tobacco plants. Furthermore, the DsIAA21 interacted with auxin response factor 5 (ARF5) in transgenic tobacco plants, suggesting that DsIAA21 might inhibit stem and root elongation via interacting with ARF5. Taken together, our data indicated that DsIAA21 was a negative regulator of plant development and suggested that amino acid differences in domain i of sIAA21 versus bIAA21 affected their response to auxin, and might play a key role in the formation of the bent culm variant in D. sinicus. Our results not only shed a light on the morphogenetic mechanism in D. sinicus, but also provided new insights into versatile function of Aux/IAAs in plants.

Hormone and carbohydrate metabolism associated genes play important roles in rhizome bud full-year germination of Cephalostachyum pingbianense

Cephalostachyum pingbianense is the only woody bamboo species that can produce bamboo shoots in four seasons under natural conditions. So far, the regulatory mechanism of shoot bud differentiation and development is unknown. In the present study, indole-3-acetic acid (IAA), zeatin riboside (ZR), gibberellin A3 (GA₃ ) and abscisic acid (ABA) contents determination, RNA sequencing and differentially expressed gene analysis were performed on dormant rhizome bud (DR), growing rhizome bud (GR), and germinative bud (GB) in each season. The results showed that the contents of IAA and ZR increased while ABA content decreased, and GA₃ content was stable during bud transition from dormancy to germination in each season. Moreover, rhizome bud germination was cooperatively regulated by multiple pathways such as carbohydrate metabolism, hormone signal transduction, cell wall biogenesis, temperature response, and water transport. The inferred hub genes among these candidates were identified by protein-protein interaction network analyses, most of which were involved in hormone and carbohydrate metabolism, such as HK and BGLU4 in spring, IDH and GH3 in winter, GPI and talA/talB in summer and autumn. It is speculated that dynamic phytohormone changes and differential expression of these genes promote the release of rhizome bud dormancy and contribute to the phenological characteristics of full-year shooting. Moreover, the rhizome buds of C. pingbianense may not suffer from ecodormancy in winter. These findings would help accumulate knowledge on shooting mechanisms in woody bamboos and provide a physiological insight into germplasm conservation and forest management of C. pingbianense.

New Genes Interacted with Recent Whole Genome Duplicates in the Fast Stem Growth of Bamboos

As drivers of evolutionary innovations, new genes allow organisms to explore new niches. However, clear examples of this process remain scarce. Bamboos, the unique grass lineage diversifying into the forest, have evolved with a key innovation of fast growth of woody stem, reaching up to 1 m/day. Here, we identify 1,622 bamboo-specific orphan genes that appeared in recent 46 million years, and 19 of them evolved from noncoding ancestral sequences with entire de novo origination process reconstructed. The new genes evolved gradually in exon−intron structure, protein length, expression specificity, and evolutionary constraint. These new genes, whether or not from de novo origination, are dominantly expressed in the rapidly developing shoots, and make transcriptomes of shoots the youngest among various bamboo tissues, rather than reproductive tissue in other plants. Additionally, the particularity of bamboo shoots has also been shaped by recent whole-genome duplicates (WGDs), which evolved divergent expression patterns from ancestral states. New genes and WGDs have been evolutionarily recruited into coexpression networks to underline fast-growing trait of bamboo shoot. Our study highlights the importance of interactions between new genes and genome duplicates in generating morphological innovation.

Comparative Transcriptomic Analysis of the Larval and Adult Stages of Taenia pisiformis

Taenia pisiformis is a tapeworm causing economic losses in the rabbit breeding industry worldwide. Due to the absence of genomic data, our knowledge on the developmental process of T. pisiformis is still inadequate. In this study, to better characterize differential and specific genes and pathways associated with the parasite developments, a comparative transcriptomic analysis of the larval stage (TpM) and the adult stage (TpA) of T. pisiformis was performed by Illumina RNA sequencing (RNA-seq) technology and de novo analysis. In total, 68,588 unigenes were assembled with an average length of 789 nucleotides (nt) and N50 of 1485 nt. Further, we identified 4093 differentially expressed genes (DEGs) in TpA versus TpM, of which 3186 DEGs were upregulated and 907 were downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes (KEGG) analyses revealed that most DEGs involved in metabolic processes and Wnt signaling pathway were much more active in the TpA stage. Quantitative real-time PCR (qPCR) validated that the expression levels of the selected 10 DEGs were consistent with those in RNA-seq, indicating that the transcriptomic data are reliable. The present study provides comparative transcriptomic data concerning two developmental stages of T. pisiformis, which will be of great value for future functional studies on the regulatory mechanisms behind adult worm pathogenesis and for developing drugs and vaccines against this important parasite.

The roles of Aux/IAA gene family in development of Dendrocalamus sinicus (Poaceae: Bambusoideae) inferred by comprehensive analysis and expression profiling

Auxin is an important hormone in many plant developmental processes. In this study, the auxin/indole acetic acid (Aux/IAA) gene family was comprehensively identified using Dendrocalamus sinicus transcriptome data. A total of 26 Aux/IAA genes (DsIAA1-DsIAA26) were mined using four conserved Aux/IAA family motifs (PF02309). They encoded hydrophilic proteins, including one or two nuclear localisation signals. The D. sinicus Aux/IAA proteins were classified into two groups, including seven sister-gene pairs based on their phylogenetic relationships. A phylogenetic tree generated by aligning 108 predicted protein sequences of 26 DsIAAs, 43 PhIAAs (Phyllostachys heterocycla), 29 AtIAAs (Arabidopsis), 31 OsIAAs (Oryza sativa) and 22 PtIAAs (Populus) revealed nine major groups. Among them, four groups, including 96 IAA proteins of all five species, suggested that the genes originated before divergence of monocots and dicots. The expression profiling in different tissues showed that most of the DsIAAs preferentially expressed in leaves and shoots, suggesting their important roles in the development of leaves and shoots in D. sinicus. Continuously high expression of DsIAA3, DsIAA4, DsIAA15, and DsIAA20 may be important for regulating shoot development in D. sinicus. These results provide useful information for further research into the function of Aux/IAA genes in woody sympodial bamboos.

Physiological Analysis and Transcriptome Profiling of Inverted Cuttings of Populus yunnanensis Reveal That Cell Wall Metabolism Plays a Crucial Role in Responding to Inversion

Inverted cuttings of Populus yunnanensis remain alive by rooting from the original morphological apex and sprouting from the base, but the lateral branches exhibit less vigorous growth than those of the upright plant. In this study, we examined the changes in hormone contents, oxidase activities, and transcriptome profiles between upright and inverted cuttings of P. yunnanensis. The results showed that the indole-3-acetic acid (IAA) and gibberellic acid (GA₃) contents were significantly lower in inverted cuttings than in upright cuttings only in the late growth period (September and October), while the abscisic acid (ABA) level was always similar between the two direction types. The biosynthesis of these hormones was surprisingly unrelated to the inversion of P. yunnanensis during the vegetative growth stage (July and August). Increased levels of peroxidases (PODs) encoded by 13 differentially expressed genes (DEGs) served as lignification promoters that protected plants against oxidative stress. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that most DEGs (107) were related to carbohydrate metabolism. Furthermore, altered activities of uridine diphosphate (UDP)-sugar pyrophosphorylase (USP, 15 DEGs) for nucleotide sugars, pectin methylesterase (PME, 7 DEGs) for pectin, and POD (13 DEGs) for lignin were important factors in the response of the trees to inversion, and these enzymes are all involved cell wall metabolism.