Yushaniadezhui (Poaceae, Bambusoideae), a new bamboo species from Yunnan, China.

A new bamboo species, Yushaniadezhui, from Kunming, Yunnan, China is described and illustrated in this paper. The new species used to be misidentified as Y.polytricha. Based on careful comparison of morphological features and molecular phylogeny evidence, we confirmed its identity as a new member of the genus Yushania. Yushaniadezhui resembles Y.maculata, Y.polytricha and Y.weixiensis in several aspects, such as culm height and branch complement structure. However, the glabrous culm leaf sheaths and internodes, the absence of auricles and oral setae on most foliage leaves, except the one-year-old foliage leaves, the pubescence on the adaxial surface of the one-year-old foliage leaves and its limestone habitat preference can readily distinguish this new species from its related taxa. Moreover, we emphasise that individuals from various populations and molecular markers with different inheritance patterns for phylogeny reconstruction should be included in new species discovery, especially in plant groups with complex evolutionary histories.

The feedstock anatomical properties determine biochar adsorption capacities: A study using woody bamboos (Bambuseae) and methylene blue as a model molecule.

Feedstock characteristics impact biochar physicochemical properties, and reproducible biochar properties are essential for any potential application. However, in most articles, feedstock aspects (i.e., taxonomic name of the species, part of the plant, and phenological phase) are scarcely reported. This research aimed at studying the effect of species and phenological stage of the feedstock on the properties of the derived biochars and, thus, adsorption capacities in water treatment. In this study, we analysed the anatomical characteristics of three different woody bamboo species [Guadua chacoensis (GC), Phyllostachys aurea (PA), and Bambusa tuldoides (BT)] in culms harvested at two different phenological phases (young and mature), and statistically correlated them with the characteristics of the six derived biochars, including their adsorption performance in aqueous media. Sclerenchyma fibres and parenchyma cells diameter and cell-wall width significantly differed among species. Additionally, sclerenchyma fibres and parenchyma cell-wall width as well as sclerenchyma fibre cell diameters are dependent on the phenological phase of the culms. Consequently, differences in biochar characteristics (i.e., yield and average pore diameter) were also observed, leading to differential methylene blue (MB) adsorption capacities between individuals at different phenological phases. MB adsorption capacities were higher for biochar produced from young culms compared to those obtained from matures ones (i.e., GC: 628.66 vs. 507.79; BT: 537.45 vs. 477.53; PA: 477.52 vs. 462.82 mg/g), which had smaller cell wall widths leading to a lower percentage of biochar yield. The feedstock anatomical properties determined biochar characteristics which modulated adsorption capacities.

Chimonobambusafarcta (Poaceae, Bambusoideae), a new species from western Guangxi, China with taxonomic notes on C.pubescens and C.luzhiensis.

Chimonobambusafarcta, a new species of temperate woody bamboos from western Guangxi, China is described and illustrated. The new species is similar to C.pubescens in the solid internodes of culms, but differs in having taller culm to 7 m with longer verrucose internodes to 23.5 cm and intranodes to 4 mm, intranode usually with a ring of 7-9 root thorns below mid-culm, abaxially brown or brown-purple verrucose-setose culm leaf sheaths with indistinct transverse veins, conspicuously developed culm leaf blades to 3.2 cm long, longer foliage leaf sheaths to 5.2 cm, larger and broader foliage leaf blades to 22 × 1.4 cm. It also somewhat resembles C.convoluta, but can be easily distinguished by having solid internodes and longer intranode 2-4 mm, very prominent nodes with supranodal ridge obviously more elevated than sheath scar, usually persistent and sometimes brownish striate culm leaf sheaths, longer culm leaf blades to 3.2 cm, and abaxially glabrous foliage leaf sheaths. Based on the morphological characteristics, this new species is assigned to C.sect.Chimonobambusa. The character description of C.pubescens are revised for its culm to 2.1 m tall, 1.1 cm in diameter and glabrous foliage leaf blades. The systematic position of C.luzhiensis is discussed, and this species is proposed as a member of C.sect.Chimonobambusa.

Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos.

MAIN CONCLUSION: CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) of woody bamboos were obviously decreased, which might regulate the internode elongation during rapid shoot growth, while CHH methylation was strongly associated with shoot developmental time or age. DNA methylation plays a critical role in the regulation of plant growth and development. Woody bamboos have a unique trait of rapid stem growth resulted from internode elongation at the shooting period. However, it is still unclear whether DNA methylation significantly controls the bamboo rapid stem growth. Here we present whole-genome DNA methylation profiles of the paleotropical woody bamboo Bonia amplexicaulis at five newly defined stages of shoot growth, named ST1-ST5. We found that CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) were significantly lower than in the incubation (ST1) and plateau stages (ST5). The changes in methylation levels mainly occurred in flanking regions of genes and gene body regions, and 23647 differentially methylated regions (DMRs) were identified between ST1 and rapid shoot growth stages (ST2-ST4). Combined with transcriptome analysis, we found that DMR-related genes enriched in the auxin and jasmonic acid (JA) signal transduction, and other pathways closely related to plant growth. Intriguingly, CHH methylation was not involved in the rapid shoot growth, but strongly associated with shoot developmental time by gradually accumulating in transposable elements (TEs) regions. Overall, our results reveal the importance of DNA methylation in regulating the bamboo rapid shoot growth and suggest a role of DNA methylation associated with development time or age in woody bamboos.

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.

Gigantochloa glabrata (Poaceae, Bambusoideae), a new bamboo species from Yunnan, China.

Gigantochloa glabrata N. H. Xia & Y. Zeng ex D. Z. Li & Z. C. Xu, sp. nov., a new species of paleotropical woody bamboo has been described and illustrated from Yunnan, China. The new species is morphologically similar to G. albociliata and G. levis, but differs from them by having erect culm sheath blades; culm sheath ligules 4-6 mm high, truncate, denticulate; and with a ring of white tomentum on the intranode and below the node. The new species was mistakenly identified as Gigantochloa albociliata in the Flora of China and was recognised with description of the vegetative characters in 2014, but it was not effectively published. Here, we designate a complete specimen with inflorescence as the type and describe it in accordance with the Code.

Two new species of Fargesia (Poaceae, Bambusoideae) from southwestern China.

Two new species of Fargesia, one from Xizang (Tibet) and one from Yunnan, China, are described and illustrated. Fargesia viridis D.Z. Li & X.Y. Ye is characterized by its densely white powder, nearly solid internodes, yellow setose sheath scar and culm sheaths, and 4-6 leaves of large size. Fargesia purpurea D.Z. Li & X.Y. Ye has thinner culms (0.5-1.4 cm in diameter), a ring of 4-5 mm tall brown setae below nodes, fewer branches, glabrous sheath scar and culm sheaths, differentiated from the related species.

A new subtribal classification of Arundinarieae (Poaceae, Bambusoideae) with the description of a new genus.

A new subtribal classification of the woody bamboo tribe Arundinarieae is proposed based on recent phylogenomic studies. Five subtribes, corresponding to the five major lineages of the ddRAD-seq based phylogenomic trees, are recognised: Arundinariinae (the leptomorph lineage), Ampelocalaminae (the ADH lineage), Gaoligongshaniinae (represented by Gaoligongshania), Hsuehochloinae (represented by Hsuehochloa) and Thamnocalaminae (the pachymorph lineage, i.e., alpine bamboos). Subtribes Ampelocalaminae, Gaoligongshaniinae and Hsuehochloinae are newly established, while the circumscriptions of subtribes Arundinariinae and Thamnocalaminae differ from the traditional classification. Subtribe Arundinariinae also includes those taxa that were previous members of the subtribe Shibataeinae. Thus, among the five redefined subtribes, Arundinariinae is the most heterogenous in terms of morphology. In Arundinarieae, rhizome type has greater implications for classification than other vegetative and reproductive characters at the subtribal level. In addition, the new monotypic genus Ravenochloa is described on the basis of its morphological characteristics and geographical distribution to accommodate the unique phylogenetic entity of Indocalamus wilsonii.

Bambusicolous Fomitiporia revisited: multilocus phylogeny reveals a clade of host-exclusive species.

FOMITIPORIA: is a genus of wood-inhabiting Hymenochaetaceae (Agaricomycetes) that includes pathogens and decomposers occurring on a wide array of plant substrates. Some species decay culms of woody bamboos, a poorly known biotic interaction. Four bambusicolous species of Fomitiporia are currently known. However, no studies concerning their phylogenetic relationships have been performed. In order to assess species boundaries and their relationships to each other, we conducted molecular phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuc 28S rDNA (28S), RNA polymerase II second largest subunit (RPB2), and translation elongation factor 1-α (TEF1), as well as morphological analyses. Four species that occur on culms of woody bamboos, F. bambusarum, F. spinescens, F. uncinata, and the new species F. bambusipileata, grouped together in an exclusive clade within a primarily Neotropical lineage. The new species differs from all other species in the group by the pileate basidiomata. Hypotheses regarding host-exclusivity are discussed.

Schizostachyum dakrongense (Poaceae, Bambusoideae), a new species from Dakrong Nature Reserve, Vietnam.

Schizostachyum dakrongense is a new species of woody bamboo from Dakrong Nature Reserve, Quang Tri Province, central Vietnam. It is closely related to S. hainanense but differs by its pseudospikelets having terminal rachilla segments with ciliate margin and 6 bracts; culm sheath with the base of the outer margin having a slight projection below its point of attachment at the node, as well as sheath blades usually less than half as long as the culm sheath proper; and leaf blades pale-puberulent and sparsely pilosulous on the abaxial surface. The new species is described and illustrated here.

Yushania tongpeii (Poaceae, Bambusoideae), a new bamboo species from north-eastern Yunnan, China.

Yushania tongpeii D.Z.Li, Y.X.Zhang & E.D.Liu, a new species of the temperate bamboo tribe Arundinarieae (Poaceae: Bambusoideae), is described and illustrated from north-eastern Yunnan, China. Yushania tongpeii is characterised by taller branching from nodes 1-2 m above the ground, usually three branches at the node, sparse purple spots and thin white powder on the internode, densely purple-spotted culm sheaths, glabrous margins of culm sheaths and tomentose leaf ligules. Based on the morphological features, this new species is assigned to section Yushania.

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.

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics.

BACKGROUND: Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their extremely slow molecular evolutionary rates, supposedly caused by their mysterious monocarpic reproduction. However, the correlation between substitution rates and flowering cycles has not been formally tested. RESULTS: Here we present 15 newly sequenced plastid genomes of temperate woody bamboos, including the first genomes ever sequenced from Madagascar representatives. A data matrix of 46 plastid genomes representing all 12 lineages of Arundinarieae was assembled for phylogenetic and molecular evolutionary analyses. We conducted phylogenetic analyses using different sequences (e.g., coding and noncoding) combined with different data partitioning schemes, revealing conflicting relationships involving internodes among several lineages. A great difference in branch lengths were observed among the major lineages, and topological inconsistency could be attributed to long-branch attraction (LBA). Using clock model-fitting by maximum likelihood and Bayesian approaches, we furthermore demonstrated extensive rate variation among these major lineages. Rate accelerations mainly occurred for the isolated lineages with limited species diversification, totaling 11 rate shifts during the tribe's evolution. Using linear regression analysis, we found a negative correlation between rates of molecular evolution and flowering cycles for Arundinarieae, notwithstanding that the correlation maybe insignificant when taking the phylogenetic structure into account. CONCLUSIONS: Using the temperate woody bamboos as an example, we found further evidence that rate heterogeneity is universal in plants, suggesting that this will pose a challenge for phylogenetic reconstruction of bamboos. The bamboos with longer flowering cycles tend to evolve more slowly than those with shorter flowering cycles, in accordance with a putative generation time effect.

The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos.

BACKGROUND: Next-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two of which are woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events. RESULTS: Transcriptomes were assembled using both reference-based and de novo methods. These two methods were tested by characterizing transcriptome content using sequence alignment to previously characterized reference proteomes and by identifying Pfam domains. Because of the striking differences in floral morphology and phenology between the herbaceous and woody bamboo lineages, MADS-box genes, transcription factors that control floral development and timing, were characterized and analyzed in this study. Transcripts were identified using phylogenetic methods and categorized as A, B, C, D or E-class genes, which control floral development, or SOC or SVP-like genes, which control the timing of flowering events. Putative nuclear orthologues were also identified in bamboos to use as phylogenetic markers. CONCLUSIONS: Instances of gene copies exhibiting topological patterns that correspond to shared phenotypes were observed in several gene families including floral development and timing genes. Alignments and phylogenetic trees were generated for 3,878 genes and for all genes in a concatenated analysis. Both the concatenated analysis and those of 2,412 separate gene trees supported monophyly among the woody bamboos, which is incongruent with previous phylogenetic studies using plastid markers.

Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences.

The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe.

Origin and evolution of fleshy fruit in woody bamboos.

Several hypotheses have been suggested to explain the origin of fleshy fruit in monocots. One is that they originated in the understory of tropical regions and another is that fleshy fruit originated in tropical rainforests where high year-round rainfall implies that seasonality is not a limiting factor. Here we identify the time of origin and ecological preferences of woody bamboos to understand the evolution of the fleshy fruit known as the bacoid caryopsis. Bayesian Inference, Maximum Likelihood and molecular dating analyses were run based on eight plastid and two nuclear regions for 68 bamboo species. Climate data and soil parameters were gathered for 464 localities for these species. The ancestral type of caryopsis was reconstructed by parsimony. According to these analyses the bacoid caryopsis may have evolved independently seven times from the Late Miocene to the Early Pliocene and Mid-Pliocene to Mid-Pleistocene via convergent evolution. Our results suggest that in bamboos neither current climatic variables nor soil parameters were significantly correlated with the appearance of this type of fruit, nor do they have a phylogenetic signal. It is remarkable, however, that the first appearance of the bacoid caryopsis in bamboos might be associated with historical preferences for warmer and wetter climate during the Miocene. Further research is needed to identify whether other factors, such as vivipary or dispersal by small animals, rather than climate, could be responsible for the evolution of this trait in woody bamboos.

Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (poaceae).

The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here, we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing eight major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large single copy and small single copy, and inverted repeat regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided strong support for most relationships despite the very short internodes and long branches in the tree. The inferred relationships were also robust to potential confounding factors (e.g., long-branch attraction) and received support from independent indels in the genome. We then added taxa from the three Arundinarieae lineages that were not included in the full-genome data set; each of these were sampled for more than 50% genome sequences. The resulting trees not only corroborated the reconstructed deep-level relationships but also largely resolved the phylogenetic placements of these three additional lineages. Furthermore, adding 129 additional taxa sampled for only eight chloroplast loci to the combined data set yielded almost identical relationships, albeit with low support values. We believe that the inferred phylogeny is robust to taxon sampling. Having resolved the deep-level relationships of Arundinarieae, we illuminate how chloroplast phylogenomics can be used for elucidating difficult phylogeny at low taxonomic levels in intractable plant groups.