Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots.

Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single-nucleus transcriptome sequencing on 10× platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single-nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.

The making of elaborate petals in Nigella through developmental repatterning.

Elaborate petals are present in many flowering plants lineages and have greatly promoted the success and evolutionary radiation of these groups. How elaborate petals are made, however, remains largely unclear. Petals of Nigella (Ranunculaceae) have long been recognized as elaborate and can thus be an excellent model for the study of petal elaboration. Here, by conducting detailed morphological, micromorphological, anatomical, developmental and evolutionary studies on the petals of Nigella species, we explored the processes, general patterns and underlying mechanisms of petal elaboration. We found that petals of Nigella are highly complex, and the complexity can be reflected at various levels. We also found that evolutionary elaboration of the Nigella petals is a gradual process, involving not only modifications of pre-existing structures but also de novo origination of new characters. Further investigations indicated that the elaboration and diversification of Nigella petals were accomplished by modifying the ancestral trajectory of petal development, a process known as developmental repatterning. Our results not only provide new insights into the development and evolution of elaborate petals, but also highlight the necessity of conducting multiple-level investigations for understanding the processes, patterns and underlying mechanisms of plant evolution.

Gains and Losses of Cis-regulatory Elements Led to Divergence of the Arabidopsis APETALA1 and CAULIFLOWER Duplicate Genes in the Time, Space, and Level of Expression and Regulation of One Paralog by the Other.

How genes change their expression patterns over time is still poorly understood. Here, by conducting expression, functional, bioinformatic, and evolutionary analyses, we demonstrate that the differences between the Arabidopsis (Arabidopsis thaliana) APETALA1 (AP1) and CAULIFLOWER (CAL) duplicate genes in the time, space, and level of expression were determined by the presence or absence of functionally important transcription factor-binding sites (TFBSs) in regulatory regions. In particular, a CArG box, which is the autoregulatory site of AP1 that can also be bound by the CAL protein, is a key determinant of the expression differences. Because of the CArG box, AP1 is both autoregulated and cross-regulated (by AP1 and CAL, respectively), and its relatively high-level expression is maintained till to the late stages of sepal and petal development. The observation that the CArG box was gained recently further suggests that the autoregulation and cross-regulation of AP1, as well as its function in sepal and petal development, are derived features. By comparing the evolutionary histories of this and other TFBSs, we further indicate that the divergence of AP1 and CAL in regulatory regions has been markedly asymmetric and can be divided into several stages. Specifically, shortly after duplication, when AP1 happened to be the paralog that maintained the function of the ancestral gene, CAL experienced certain degrees of degenerate evolution, in which several functionally important TFBSs were lost. Later, when functional divergence allowed the survival of both paralogs, CAL remained largely unchanged in expression, whereas the functions of AP1 were gradually reinforced by gains of the CArG box and other TFBSs.

Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae).

Absence of petals, or being apetalous, is usually one of the most important features that characterizes a group of flowering plants at high taxonomic ranks (i.e., family and above). The apetalous condition, however, appears to be the result of parallel or convergent evolution with unknown genetic causes. Here we show that within the buttercup family (Ranunculaceae), apetalous genera in at least seven different lineages were all derived from petalous ancestors, indicative of parallel petal losses. We also show that independent petal losses within this family were strongly associated with decreased or eliminated expression of a single floral organ identity gene, APETALA3-3 (AP3-3), apparently owing to species-specific molecular lesions. In an apetalous mutant of Nigella, insertion of a transposable element into the second intron has led to silencing of the gene and transformation of petals into sepals. In several naturally occurring apetalous genera, such as Thalictrum, Beesia, and Enemion, the gene has either been lost altogether or disrupted by deletions in coding or regulatory regions. In Clematis, a large genus in which petalous species evolved secondarily from apetalous ones, the gene exhibits hallmarks of a pseudogene. These results suggest that, as a petal identity gene, AP3-3 has been silenced or down-regulated by different mechanisms in different evolutionary lineages. This also suggests that petal identity did not evolve many times independently across the Ranunculaceae but was lost in numerous instances. The genetic mechanisms underlying the independent petal losses, however, may be complex, with disruption of AP3-3 being either cause or effect.

Gelidocalamuszixingensis (Poaceae, Bambusoideae, Arundinarieae), a new species from southern China revealed by morphological and molecular evidence.

The genus Gelidocalamus T. H. Wen, endemic to southern China, is a small but taxonomically problematic genus of Arundinarieae (Poaceae, Bambusoideae). During field work, a population of Gelidocalamus from Zixing, Hunan, was discovered, appearing to be distinct from our previously identified collection. Comparisons of the population of Zixing were performed by using scanning electron microscopy (SEM) and a plastid genome-based phylogeny. Morphologically, it was mostly similar to G.multifolius, but differed by culm leaf erect with densely white pubescence, apical branch sheath much longer than the internodes and foliage leaf larger. Phylogenetically, the new species was well-supported as a sister to the clade of G.multifolius + G.tessellatus, and the above three taxa were clustered in the Shibataea clade (IV) of Arundinarieae. Thus, the new species, formally named as Gelidocalamuszixingensis W.G.Zhang, G.Y.Yang & C.K.Wang, was described and illustrated herein.

Karyotype and genome size variation in Delphinium subg. Anthriscifolium (Ranunculaceae).

Five taxa of Delphiniumsubg.Anthriscifolium have been karyologically studied through chromosome counting, chromosomal measurement, and karyotype symmetry. Each taxon that we investigated has a basic chromosome number of x = 8, D.anthriscifoliumvar.savatieri, D.anthriscifoliumvar.majus, D.ecalcaratum, and D.callichromum were diploid with 2n = 16, while D.anthriscifoliumvar.anthriscifolium was tetraploid with 2n = 32. Monoploid chromosome sets of the investigated diploid taxa contained 1 metacentric chromosome, 3 submetacentric chromosomes, and 4 subtelocentric chromosomes. Higher interchromosomal asymmetry (CVCL) was present in D.ecalcaratum and D.callichromum than in other taxa. The highest levels of intrachromosomal asymmetry (MCA) and heterogeneity in centromere position (CVCI) were found in D.anthriscifoliumvar.majus. Diploid and tetraploid genome sizes varied by 3.02-3.92 pg and 6.04-6.60 pg, respectively. Karyotype and genome size of D.anthriscifoliumvar.savatieri, D.anthriscifoliumvar.majus, D.callichromum, and D.ecalcaratum were reported for the first time. Finally, based on cytological and morphological data, the classification of Delphiniumanthriscifolium was revised.

Gelidocalamusalbozonatus (Poaceae, Bambusoideae), a new species from the southeast of Chongqing, China, and analysis of the morphological diversity in the core group of Gelidocalamus.

Gelidocalamusalbozonatus W. G. Zhang, S. R. Yi & Y. L. Li, a new species of Gelidocalamus, collected from Pengshui County of Chongqing City in China, was described and illustrated herein. In this study, key morphological characters were compared between the new species and other eight "gelido-" members of Gelidocalamus. By using scanning electron microscopy (SEM), its leaf epidermal characters were observed in comparison with those of another three Gelidocalamus representatives. Our results show that the new taxon has the typical characteristics of the genus Gelidocalamus, both macromorphologically and micromorphologically. Moreover, it was most similar to G.tessellatus, but differed by a ring of white tomenta below per node, culm sheath base with densely purple verrucous setae and foliage leaf blades mesophyll.

Complete chloroplast genome sequence and phylogenetic analysis of Chimonobambusa sichuanensis (Bambusoideae).

Chimonobambusa sichuanensis is an ornamental shrubby bamboo endemic to southern China. In this study, the complete chloroplast genome (cpDNA) sequence of Chimonobambusa sichuanensis was first reported. The cpDNA is 139,594 bp in length, including a small single-copy (SSC) region of 12,820 bp and a large single-copy (LSC) region of 83,196 bp, which were separated by a pair of inverted repeat (IR) regions of 21,789 bp. The genome contains 140 genes, consisting of 93 protein-coding genes, seven ribosomal RNA (rRNA) genes, and 40 transfer RNA (tRNA) genes. The phylogenetic analysis showed that C. sichuanensis is highly clustered in the Phyllostachys clade, sister to C. tumidissinoda.

The complete chloroplast genome of Phyllostachys edulis f. curviculmis (Bambusoideae): a newly ornamental bamboo endemic to China.

Phyllostachys edulis (Bambusoideae) is a temperate woody bamboo with a long history of cultivation in China. Phyllostachys edulis f. curviculmis is the latest new forma that repored in 2018. Here, we performed the complete chloroplast genomes of P. edulis and P. edulis f. curviculmis using genome skimming. The length of two chloroplast genomes was 139,678 bp, and their GC contents were 38.9%. The sequences of each species contained 132 unique genes, including 39 tRNA, eight rRNA, and 85 protein-coding genes. Moreover, in subspecies-level, P. edulis 'Pachyloen' and P. edulis f. curviculmis are identical to P. edulis in the terms of chloroplast genome size, structure, and composition, further indicating their affinity.

The complete chloroplast genome sequence of Gelidocalamus xunwuensis (Bambusoideae: Arundinarieae): a shrubby bamboo endemic to China.

The complete chloroplast genome sequence of Gelidocalamus xunwuensis, firstly determined here, is 139,705 bp in length, inclusive of a pair of inverted repeat (IR, 21,817 bp) regions separated by a small single copy (SSC, 12,803 bp) and a large single copy (LSC, 83,268 bp). It contains 132 genes, such as 85 CDS, 8 rRNA genes, and 39 tRNA genes, respectively. The phylogenetic analysis shows that G. xunwuensis is highly clustered in the shibataea clade (III) of Arundinarieae, sister to the clade of G. tessellatus + Ferrocalamus rimosivaginus.

Complete chloroplast genome of a rare deciduous tree species, Sinomanglietia glauca (Magnoliaceae).

The complete chloroplast genome of a rare deciduous tree species with ornamental value, Sinomanglietia glauca, was first determined. It was 160,170 bp in length, including a pair of inverted repeat (IR, 26,567 bp) regions separated by a small single copy (SSC, 18,842 bp) sequence and a large single copy (LSC, 88,194 bp) sequence. The chloroplast genome contained 132 genes, consisting of 87 CDS, 8 rRNA genes, and 37 tRNA genes. Thirty-four SSR sites were detected in the chloroplast genome. The phylogenetic analysis revealed that all sampled Manglietia species were clustered together, and S. glauca was placed as sister to the clade Manglietia, indicated that the genus Sinomanglietia may be legitimate and should be recovered.

Gelidocalamus xunwuensis (Poaceae, Bambusoideae), a new species from southeastern Jiangxi, China.

Gelidocalamus xunwuensis W.G.Zhang & G.Y.Yang, a new species collected from Xunwu County of Jiangxi Province in China, is described and illustrated. The new species is similar to G. stellatus in the habit, but differs by internodes sparsely hairy with granuliferous warts, culm sheath stiffly hairy, culm sheath blade broadly lanceolate to narrowly triangular, each node with a ring of appressed trichomes below, foliage leaves broadly lanceolate to narrowly oblong, and new shoots occurring in late October.

Flexibility in the structure of spiral flowers and its underlying mechanisms.

Spiral flowers usually bear a variable number of organs, suggestive of the flexibility in structure. The mechanisms underlying the flexibility, however, remain unclear. Here we show that in Nigella damascena, a species with spiral flowers, different types of floral organs show different ranges of variation in number. We also show that the total number of organs per flower is largely dependent on the initial size of the floral meristem, whereas the respective numbers of different types of floral organs are determined by the functional domains of corresponding genetic programmes. By conducting extensive expression and functional studies, we further elucidate the genetic programmes that specify the identities of different types of floral organs. Notably, the AGL6-lineage member NdAGL6, rather than the AP1-lineage members NdFL1/2, is an A-function gene, whereas petaloidy of sepals is not controlled by AP3- or PI-lineage members. Moreover, owing to the formation of a regulatory network, some floral organ identity genes also regulate the boundaries between different types of floral organs. On the basis of these results, we propose that the floral organ identity determination programme is highly dynamic and shows considerable flexibility. Transitions from spiral to whorled flowers, therefore, may be explained by evolution of the mechanisms that reduce the flexibility.