Temperate Woody Bamboos Research Articles

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.

Taxonomic revision of the genus Chimonocalamus (Arundinarieae, Bambusoideae, Poaceae) in Thailand

Chimonocalamus is a genus in the Arundinarieae (the tribe of temperate woody bamboos), distributed in the Eastern Himalayas, India, Myanmar, China, Thailand, and Vietnam. Distinguishing characters of the genus include pachymorph rhizomes, rings of root thorns at lower culm nodes, a branch complement of 3–5 subequal branches, paniculate inflorescences, and spikelets with 2 glumes and 3–6 florets. Taxonomic knowledge of Chimonocalamus in mainland Southeast Asia has grown as new species were reported from Thailand and Vietnam, adding to those previously documented mainly in China and India. Such a situation supports an increased understanding in the geographic distribution and diversity of the group. The objective of this paper is to update the Chimonocalamus account for Thailand and summarize taxonomic information pertinent to future studies. Here, our taxonomic revision of Chimonocalamus in Thailand includes three species, C. auriculatus, C. elegans and C. gallatlyi; the latter is a new record for Thailand. Nomenclatural treatments, morphological descriptions, a photographic illustration of C. gallatlyi, and a current distribution map of three species are presented.

Species distribution modelling and population genetic analysis ofYushania anceps; an endemic temperate woody bamboo of the Uttarakhand Himalayas

AbstractYushania ancepsis a temperate woody bamboo taxon of high socio-economic importance occurring in the sub-alpine zone of the western Himalayas. This study was carried out to delineate the potential distribution ofY. ancepsin the western Himalayas through species distribution modelling (SDM), and genetic characterization using sequence-tagged microsatellite (STMS) markers. The present study revealed an endemic distribution of this species in the Uttarakhand Himalayas, with an estimated area of 211.59 km2. The maximum probability of occurrence was recorded in the moderately dense forests between the altitudinal ranges of 2500 and 2700 m. The model output was well supported with high values of different statistical measures, such as the AUC (0.911) and Kappa coefficient (K= 0.513). Environmental variables related to precipitation, temperature and topography were identified as the most contributory in current SDM. In addition, diversity measures, namely allelic richness (Ar), expected heterozygosity (He), and fixation index (FST), were calculated in five sampled populations with eight STMS markers, which indicated high genetic diversity (Ar = 4.24; He = 0.689) and little differentiation (FST= 0.062). The diversity maps displayed that the populations located in the Kumaon region captured relatively more genetic diversity than the Garhwal region. Further, genetic clustering and STRUCTURE analysis revealed a substantial level of genetic admixing across the analysed populations, and as a result, no sub-structuring was detected. Due to the rare and endemic distribution ofY. anceps, it requires immediate conservation measures, and the knowledge base generated here will be of paramount importance to forest managers, researchers and policymakers.

Tallapoosa Cane (Arundinaria alabamensis), a new species of temperate bamboo (Poaceae: Bambusoideae) from East Central Alabama

Arundinaria alabamensis (Tallapoosa Cane) is described as a new species of North American temperate woody bamboo. Recognition of this species is consistent with molecular genetic data that suggests an origin through hybridization and subsequent diversification, as it bears a unique chloroplast DNA haplotype most similar to A. gigantea (River Cane), nuclear DNA haplotypes that cluster with A. appalachiana (Hill Cane) and A. tecta (Switch Cane), and a distinct AFLP fingerprint. Tallapoosa Cane can be distinguished from the other North American Arundinaria by a combination of vegetative characters including larger leaf size, foliage sheath pubescence, and a distinctive branch complement. This Alabama endemic is currently known from eight populations across four counties: Cleburne (3), Lee (3), Macon (1), and Randolph (1). The new species is described and compared with the related species of Arundinaria, and an identification key is included along with a comparative table based on morphological characters.

Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 “perfect-copy” syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.

Population genetic analysis illustrated a high gene diversity and genetic heterogeneity in Himalayacalamus falconeri: a socio-economically important Indian temperate woody bamboo taxon

Population genetic analysis illustrated a high gene diversity and genetic heterogeneity in Himalayacalamus falconeri: a socio-economically important Indian temperate woody bamboo taxon

Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae).

The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.

<p><strong><em>Yushania doupengshanensis</em> (Poaceae, Bambusoideae), a new bamboo species from south Guizhou, China</strong></p>

Yushania doupengshanensis Y.Y. Zhang et N.H. Xia, a new species of the temperate woody bamboo tribe Arundinarieae (Poaceae: Bambusoideae), is described and illustrated from south Guizhou, China. Yushania doupengshanensis is characterised by long-necked rhizomes, usually a single branch at each branching node, densely white puberulous and thin white powdery internodes, tardily deciduous culm sheaths, densely ciliate culm-sheath margins, 6‒12 leaves per ultimate branch, densely puberulous and 8‒9 mm long pseudopetioles. Based on the morphological features, this new species is assigned to section Yushania.

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.

Tropical plants evolve faster than their temperate relatives: a case from the bamboos (Poaceae: Bambusoideae) based on chloroplast genome data

The evolutionary speed hypothesis (ESH) states that the molecular evolutionary rates of plants in the warm areas are higher than that in the cool areas. Nevertheless, largely due to the scarcity of molecular data from lower taxonomic lineages, ESH remains elusive in plants. In this study, we comprehensively conducted genome-wide comparative analyses of a total of 76 chloroplast (cp) genomes of the bamboos (Poaceae: Bambusoideae), with 10 of them newly generated, to test the ESH via investigating the potential association between their cp genome evolutionary rate and geographical distribution pattern. The results showed extreme heterogeneity of the evolutionary rate within the bamboos, with the lowest value found in temperate bamboos (tribe Arundinarieae) being approximately 1/4 of that in the tropical ones (tribe Olyreae). All the 91 non-coding loci and 75 coding loci evolve consistently faster in tribe Olyreae than that in tribe Arundinarieae. Most of the non-coding (82 out of 91) and coding (73 out of 75) loci in the tropical woody bamboos (tribe Bambuseae) also evolve faster than those in the temperate woody bamboos (tribe Arundinarieae). Moreover, the split of tropical and temperate bamboos was apparently accompanied with the change of cp genome evolutionary rate. This is by far the first case using cp genome data to support the ESH via showing the tropical plants evolve faster than their closely related temperate ones, and will shed new light on our understanding of ESH and the adaptation of plants.

Phylogeny of Fargesia (Poaceae: Bambusoideae) and infrageneric adaptive divergence inferred from three cpDNA and nrITS sequence data

Fargesia, a temperate woody bamboo genus, is one of the largest genera and constitutes a taxonomically problematic group due to unusual life cycles and the rarity of flowering. We explored phylogenetic relationships within Fargesia and its allies based on sequence data from three cpDNA regions (matK, psbA-trnH and trnL-trnF) and one nuclear region (nrITS). A representative sample of 49 species, including 36 Fargesia and nine Yushania, were sampled, and maximum parsimony, maximum likelihood and Bayesian inference were used to reconstruct the phylogeny of Fargesia. The results suggest that Fargesia is polyphyletic, with F. crassinoda and F. damuniu in the Thamnocalamus clade, F. ampullaris, F. semiorbiculata, F. gyirongensis and F. collaris in the Drepanostachyum + Himalayacalamus clade, and the rest of species of Fargesia and all sampled species of Yushania in a Fargesia + Yushania clade, which was further divided into weakly supported Fargesia spathe and non-spathe clades. Species in the Fargesia spathe clade have the derived “spathe-like leaf sheath syndrome,” which may have evolved as a result of an adaptive advantage of compressed inflorescences in colder temperatures.

Chimonocalamus auriculatus, one more new temperate woody bamboo species of the genus (Poaceae: Bambusoideae: Arundinarieae) described from Thailand

Chimonocalamus auriculatus, a temperate woody bamboo (Arundinarieae), from the border between Thailand and Lao PDR, is described and illustrated here. In its vegetative state, the new species can be distinguished from all the other Chimonocalamus species by its conspicuous auricles and oral setae (bristles) on the culm leaf sheath.

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

BackgroundHeterogeneous 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.ResultsHere 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.ConclusionsUsing 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.

In search of the phylogenetic affinity of the temperate woody bamboos from Madagascar, with description of a new species (Bambusoideae, Poaceae)

AbstractSix temperate woody bamboos (Arundinarieae, Bambusoideae) from Madagascar were described in the genus Arundinaria during the 1920s to 1960s. However, recent phylogenetic studies imply that Arundinaria is restricted to North America, and taxonomic affiliation of the Malagasy temperate woody bamboos remained ambiguous. In search of phylogenetic affinity of these bamboos, herbarium observation, fieldwork, and molecular phylogenetic analysis have been carried out. Four of them and one potential new species were sampled for molecular phylogenetic analyses in the context of the tribe Arundinarieae. Maximum likelihood and Bayesian analyses indicated that those species were closely related to Oldeania alpina distributed in continental Africa, but not Arundinaria, Bergbambos, Fargesia (including Sinarundinaria), Thamnocalamus, or Yushania, in which they were placed at one time or another. On the grounds of molecular phylogeny, morphology, and phytogeography, the Malagasy temperate woody bamboos should be treated as members of the genus Oldeania. Arundinaria humbertii and A. ambositrensis are conspecific. A new species, Oldeania itremoensis, is described and illustrated. The other two temperate woody bamboo species in Madagascar not sampled in the molecular phylogeny are also transferred to Oldeania on the basis of morphology.

Chimonocalamus elegans, a new temperate woody bamboo species (Poaceae: Bambusoideae) from Doi Phu Kha National Park, Thailand

Chimonocalamus elegans, a tentatively endemic new species of temperate woody bamboos from Northern Thailand is described and illustrated. The new species differs from other members of Chimonocalamus by its glabrous nodes, culm leaf sheaths with narrow apex (3−4 mm) and 4−7 mm long ligules.

Evolution of genome sizes in Chinese Bambusoideae (Poaceae) in relation to karyotype

DNA contents of Chinese 134 bamboo species were first time announced, and FISH of 45S rDNA shows that paleotropical woody bamboo species may be originated from a multi-source system. Woody bamboo mainly includes two types of species: the temperate woody bamboo and the tropical woody bamboo. Both vary widely in genome sizes, chromosome number, and ploidy. In this study, the DNA contents of 135 bamboo species (22 genera) mainly distributed in China were analyzed by the flow cytometry. The DNA contents of the 134 bamboo species were first time announced. In contrast to the paleotropical woody bamboos, the temperate woody species is larger in genome size. Both the average arm ratio and the average symmetric coefficient of karyotype of the temperate woody species are less than those of the paleotropical woody bamboos, suggesting that the karyotypes of temperate woody bamboo species are more symmetrical than that of paleotropical bamboos. Also, FISH (fluorescence in situ hybridization) was applied to evaluate the distribution of 45S rDNA in the chromosomes of the representative bamboo species. Only one pair of sites was detected for 45S rDNA in temperate woody bamboo species, while three pairs of sites in paleotropical woody bamboo species, implying that the paleotropical woody bamboo species may be originated from a multi-source system. This study exposed a corner of the complex genomic relationships in the woody bamboos and provided an initial framework for future phylogenic studies.

Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis

We explored phylogenetic relationships among the twelve lineages of the temperate woody bamboo clade (tribe Arundinarieae) based on plastid genome (plastome) sequence data. A representative sample of 28 taxa was used and maximum parsimony, maximum likelihood and Bayesian inference analyses were conducted to estimate the Arundinarieae phylogeny. All the previously recognized clades of Arundinarieae were supported, with Ampelocalamus calcareus (Clade XI) as sister to the rest of the temperate woody bamboos. Well supported sister relationships between Bergbambos tessellata (Clade I) and Thamnocalamus spathiflorus (Clade VII) and between Kuruna (Clade XII) and Chimonocalmus (Clade III) were revealed by the current study. The plastome topology was tested by taxon removal experiments and alternative hypothesis testing and the results supported the current plastome phylogeny as robust. Neighbor-net analyses showed few phylogenetic signal conflicts, but suggested some potentially complex relationships among these taxa. Analyses of morphological character evolution of rhizomes and reproductive structures revealed that pachymorph rhizomes were most likely the ancestral state in Arundinarieae. In contrast leptomorph rhizomes either evolved once with reversions to the pachymorph condition or multiple times in Arundinarieae. Further, pseudospikelets evolved independently at least twice in the Arundinarieae, but the ancestral state is ambiguous.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae).

Premise of the study:Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources.Methods and Results:A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae).Conclusions:WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus.

Taxonomic Revision of the Temperate Woody Bamboo Genus Kuruna (Poaceae: Bambusoideae: Arundinarieae)

Abstract Previous molecular phylogenetic analyses based on plastid DNA sequence data supported the recognition of Kuruna as a new temperate woody bamboo (Arundinarieae) genus, representing the twelfth major linage of Arundinarieae. Kuruna is distinguished by a combination of vegetative and reproductive characters including features of rhizomes, branching and synflorescences. Here seven species, distributed in Sri Lanka and southern India, are included in this genus: Kuruna debilis, K. densifolia, K. floribunda, K. scandens, K. walkeriana, K. wightiana (here transferred to Kuruna), and the newly described K. serrulata. This revision includes an updated description of the genus, detailed descriptions for all seven species, line illustrations for all species, and a morphological key for their identification.

Genome skimming reveals the complete chloroplast genome of Ampelocalamus naibunensis (Poaceae: Bambusoideae: Arundinarieae) with phylogenomic implication

Ampelocalamus naibunensis is one drooping bamboo with an important ornamental value endemic to Taiwan Island. To date, the genetic and genomic information of this species is little known. Here we characterized the complete chloroplast genome of A. naibunensis using genome skimming approach. The complete chloroplast genome is 139,860 bp, with a large single copy region (LSC) of 83,380 bp and a small single copy region (SSC) of 13,014 bp separated by a pair of inverted repeats (IRs) of 21,822 bp. The genome encodes a total of 129 genes, of which 111 are unique, containing 76 protein-coding genes, 4 ribosomal RNAs and 31 transfer RNAs. Sixteen distinct genes contain one or two introns, and the GC content of the cp genome is 38.9%. Phylogenomic analysis strongly supports the placement of A. naibunensis in the Chimonocalamus lineage (III), distantly related to A. calcareus (XI) within temperate woody bamboos.