Plant-microbe interactions are fundamental to biodiversity maintenance and ecosystem functioning, and their assembly is shaped by a complex interplay of ecological and evolutionary processes. However, how these forces jointly influence ectomycorrhizal (EcM) fungal communities, especially those dominant in subalpine forests, remains poorly understood. To address this, we investigated EcM fungal communities associated with 11 species of Pinaceae (Abies, Picea and Pinus) across 195 monodominant stands in the subalpine forests of the Qinghai-Tibetan Plateau. We found that all pine species are consistently associated with a broad phylogenetic range of EcM fungal lineages, and that pine-EcM association networks exhibit low connectance, indicating low partner specificity. Variation in fungal community structure was significantly influenced by host identity, environmental factors and spatial distribution, but not by host phylogenetic relatedness. Notably, fungal taxa from three dominant lineages (Sebacina, Russula and Inocybe) were clustered phylogenetically with globally distributed Pinaceae-associated taxa, pointing to evolutionarily conserved symbiotic associations across biogeographic regions. Together, these results indicate that EcM fungal communities in subalpine Pinaceae forests are assembled through a combination of evolutionary conservatism and environmental filtering. The persistent association with key EcM fungi across Pinaceae species underscores their essential role in supporting tree physiology and forest ecosystem stability in subalpine environments. What governs the formation of symbiotic partnerships between microbes and their hosts? Drawing on a regional-scale study across the Tibetan Plateau, we demonstrate that the assembly of pine-ectomycorrhizal fungal communities is not shaped by a single force. Rather, their structure emerges from the interplay between evolutionary conservatism and environmental filtering. (sic)(sic):(sic)(sic)-(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic).(sic)(sic), (sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(EcM)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic).(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)11(sic)(sic)(sic)(sic)(Abies),(sic)(sic)(sic)(Picea)(sic)(sic)(sic)(Pinus)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic), (sic)(sic)(sic)(sic)(sic)195(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)EcM(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic).(sic)(sic)(sic)(sic):1)(sic)(sic)(sic)(sic)(sic)(sic)(sic)EcM(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic), (sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic), (sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic).2)EcM(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic),(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic), (sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic).3)(sic)(sic)(sic)(sic)3(sic)(sic)(sic)EcM(sic)(sic)(sic)(sic), (sic)(sic)(sic)(sic)(sic)(Sebacina),(sic)(sic)(sic)(Russula)(sic)(sic)(sic)(sic)(sic)(Inocybe), (sic)(sic)(sic)(sic)(sic)EcM(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic), (sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic).(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic), (sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)EcM(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic), (sic)(sic)EcM(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic)(sic).

The vast majority of land plants transfer part of the organic carbon they produce by photosynthesis to arbuscular mycorrhizal (AM) fungi inside their root cells; the fungi in turn help plants to take up nutrients and water from the soil. This carbon can subsequently be acquired from mycorrhizal fungi by rare nonphotosynthetic 'mycoheterotrophic' plants that tap into the same fungal network. However, recent findings suggest that carbon uptake from AM fungi may exist among some green plants too. If so, this would qualify them as partial mycoheterotrophs (mixotrophs) rather than as pure autotrophs. Here, we discuss the evolutionary, ecophysiological, morphological, genetic, and environmental evidence for the existence and prevalence of this trait. We conclude that there is strong, albeit indirect, evidence for its existence, although its taxonomic distribution remains to be determined. This knowledge gap currently prevents us from inferring the magnitude of AM partial mycoheterotrophy in terrestrial ecosystems, which in turn severely limits our understanding of its role in plant establishment and survival and in ecosystem structure and function.

Mycorrhizal symbioses are prevalent in terrestrial ecosystems and play essential roles in plant nutrition and health. However, the relative importance of plant evolutionary history, physiology, and eco-geographical factors in shaping mycorrhizal fungal community assembly remains poorly understood. Here, we investigate how plant phylogeny, trophic mode, biogeographic distribution and environmental niche collectively influence the diversity and composition of mycorrhizal fungal communities across the Orchidaceae, spanning broad phylogenetic and ecological scales. By using family-wide orchid-fungal associations and global occurrence data, our analyses showed that the variation in fungal diversity and community structure can be partially explained by orchids’ trophic mode, biogeographic distribution and environmental niche, but not by their overall phylogenetic relatedness. Among trophic modes, partially mycoheterotrophic orchids exhibited the highest level of fungal diversity (the lowest level of fungal specificity) in association with a broad range of phylogenetically dispersed fungal partners. Between biogeographical regions, a significantly higher level of fungal specificity was found for orchid species distributed in Australia than those in Eurasia and Africa. Furthermore, multivariate analyses showed that a small portion of the variation in fungal community structure was significantly related to broad climate, soil and vegetation variables, indicating the existence of large-scale habitat filtering on orchid mycorrhizal communities. Altogether, our findings indicate that mycorrhizal communities in the orchid family are likely shaped by multiple, intertwined factors related to orchid ecophysiology and biogeography on a global scale.

The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.

BACKGROUND:Root activity creates a unique microbial hotspot in the rhizosphere, profoundly regulating soil activity and associated soil multifunctionality (SMF), the ability of soil to deliver multiple functions or services simultaneously. However, empirical studies on the characteristics of SMF in the rhizosphere and bulk soil and their microbial regulatory mechanisms remain scarce. METHODS:To address this gap, we conducted a field sampling campaign in an alpine forest on the eastern Tibetan Plateau. Soil abiotic and biotic properties, including soil nutrient availability, enzyme activities and microbial attributes were examined to compare the characteristics of SMF in the rhizosphere and bulk soil of Abies georgei, and to explore how microbial mechanisms drive SMF in each compartment. RESULTS:We found that the rhizosphere consistently exhibited higher SMF than bulk soil, highlighting its enhanced functional potential regardless of environmental variation. The relationship between microbial diversity and SMF was compartment-specific: bacteria diversity was strongly associated with SMF in the rhizosphere, while fungal diversity was closely linked to SMF in the bulk soil. Furthermore, microbial biomass, particularly fungal biomass, had a strong influence on SMF in both rhizosphere and bulk soils. Structural equation modeling revealed that the relationship between soil diversity and SMF were primarily mediated by variations in soil abiotic properties, including soil pH in the bulk soil, and soil moisture and clay content in the rhizosphere. CONCLUSIONS:Our findings demonstrate that microbial contributions to soil multifunctionality are compartment-dependent and emphasize the need to integrate the rhizosphere perspective into biodiversity-multifunctionality frameworks for improving predictions of soil functions in terrestrial ecosystems.

The prevalence and potential functions of common mycorrhizal networks, or the ‘wood-wide web’, resulting from the simultaneous interaction of mycorrhizal fungi and roots of different neighbouring plants have been increasingly capturing the interest of science and society, sometimes leading to hyperbole and misinterpretation. Several recent reviews conclude that popular claims regarding the widespread nature of these networks in forests and their role in the transfer of resources and information between plants lack evidence. Here we argue that mycoheterotrophic plants associated with ectomycorrhizal or arbuscular mycorrhizal fungi require resource transfer through common mycorrhizal networks and thus are natural evidence for the occurrence and function of these networks, offering a largely overlooked window into this methodologically challenging underground phenomenon. The wide evolutionary and geographic distribution of mycoheterotrophs and their interactions with a broad phylogenetic range of mycorrhizal fungi indicate that common mycorrhizal networks are prevalent, particularly in forests, and result in net carbon transfer among diverse plants through shared mycorrhizal fungi. On the basis of the available scientific evidence, we propose a continuum of carbon transfer options within common mycorrhizal networks, and we discuss how knowledge on the biology of mycoheterotrophic plants can be instrumental for the study of mycorrhizal-mediated transfers between plants. In this Perspective, Vincent Merckx and colleagues discuss an important but overlooked aspect of mycorrhizal interactions, mycoheterotrophy, in the context of recent arguments about the importance of these interactions to forest functioning.

AimUnderstanding the various factors that contribute to the distribution and geographical ranges of plant and animal species has been a central issue in ecology, evolution and biogeography for more than two centuries. In this study, we investigated whether (i) niche breadth is phylogenetically conserved, (ii) niche overlap is negatively correlated with orchid evolutionary distance, and (iii) more recently diverged sister species show more niche overlap compared to older sister species.LocationEurope.TaxonOrchids (Orchidaceae).MethodsEcological niche models were created for 107 European orchid species distributed across 17 genera using occurrence and environmental data. A time-calibrated phylogeny was reconstructed and the phylogenetic signal for range size and niche breadth was estimated. Phylogenetic distances among species were calculated to test the hypothesis that niche overlap is explained by evolutionary history. Finally, we investigated whether the divergence age of sister taxa was negatively related to niche overlap.ResultsRange size and niche breadth in both geographical and environmental space varied by more than three orders of magnitude and were strongly correlated with each other. We did not find strong evidence for phylogenetic conservatism in range size, niche breadth and niche overlap. However, sister taxa pairs with older divergence age showed less overlap in their environmental niche compared to more recently diverged sister taxa.Main ConclusionsWe conclude that orchid species that have broader ecological niches tend to display larger range sizes. Our results further show that the current distribution of orchid species across the European continent is best explained by recent speciation events and relative rapid adaptation to local environmental conditions, while deep-level phylogenetic relationships are not correlated with ecological niche breadth.

Stable isotope signatures of fungal sporocarps have been instrumental in identifying carbon gains of chlorophyllous orchids from a fungal source. Yet, not all mycorrhizal fungi produce macroscopic sporocarps and frequently fungi of different taxa occur in parallel in orchid roots. To overcome this obstacle, we investigated stable isotope signatures of fungal pelotons extracted from orchid roots and compared these data to the respective orchid and reference plant tissues. Anoectochilus sandvicensis and Epipactis palustris represented specialized or unspecialized rhizoctonia-associated orchids. Epipactis atrorubens and Epipactis leptochila are orchids considered ectomycorrhiza-associated with different preferences for Basidio- and Ascomycota. 13 C enrichment of rhizoctonia pelotons was minor compared with plant tissues and significantly lower than enrichments of pelotons from ectomycorrhizal Epipactis species. 15 N values of pelotons from E. leptochila and E. atrorubens showed similar patterns as known for respective sporocarps of ectomycorrhizal Ascomycota and Basidiomycota, however, with an offset towards lower 15 N enrichments and nitrogen concentrations. Our results suggest an explicit fungal nutrition source of orchids associated with ectomycorrhizal fungi, whereas the low 13 C enrichment in rhizoctonia-associated orchids and fungal pelotons hamper the detection of carbon gains from fungal partners. 15 N isotopic pattern of orchids further suggests a selective transfer of 15 N-enriched protein-nitrogen into orchids.

Old trees are irreplaceable natural resources that provide multifaceted benefits to humans. Current conservation strategies focus primarily on large-sized trees that were often considered old. However, some studies have demonstrated that small trees can be more than thousands of years old, suggesting that conventional size-focused perceptions may hamper the efficiency of current conservation strategies for old trees. Here, we compiled paired age and diameter data using tree-ring records sampled from 121,918 trees from 269 species around the world to detect whether tree size is a strong predictor of age for old trees and whether the spatial distribution of small old trees differs from that of large old trees. We found that tree size was a weak predictor of age for old trees, and diameter explained only 10% of the total age variance of old trees. Unlike large-sized trees that are mainly in warm, wet environments and protected, small old trees are predominantly in cold, dry environments and mostly unprotected, indicating that size-focused conservation failed to protect some of the oldest trees. To conserve old trees, comprehensive old-tree recognition systems are needed that consider not only tree size but also age and external characteristics. Protected areas designed for small old trees are urgently needed.

Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances.Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding.Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families.This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.

Orchid mycorrhiza forms unique symbiotic associations between members of the Orchidaceae and multiple ecological guilds of fungi. Because orchids associate with a wide variety of fungi with different ecological functions, they represent an ideal study system to address fundamental questions about the evolution and ecophysiology of mycorrhizal symbiosis. Although it is well established that shifts in mycorrhizal associations are linked to transitions in plant trophic mode, it remains unclear what ecological drivers promote these evolutionary changes. Here, we investigated mycorrhizal communities and isotope signatures across six populations of the terrestrial orchid Neottia ovata growing under contrasting light conditions in temperate Europe. We hypothesized that plants growing in forests would associate with different mycorrhizal fungi than plants occurring in grasslands and that the limited light availability in forests leads to a higher contribution of fungi to the carbon budget of orchids. Our results showed that N. ovata predominantly associated with rhizoctonia fungi of the family Serendipitaceae in both habitats, but plants in forests also recruited ectomycorrhizal fungi. Root communities highly resembled soil communities and variation in root communities was significantly related to habitat type and edaphic factors. In contrast, isotope signatures (C-13, N-15, H-2 and O-18) and N concentration showed no significant relationship with habitat type. In addition, both C-13 and H-2 were not significantly correlated to habitat's light availability. Although it has been suggested that the presence of a wide variety of ectomycorrhizal fungi in root communities of orchids can serve as a precursor for evolutionary shifts to partial mycoheterotrophy (mixotrophy), the presence or absence of ectomycorrhizal fungi did not substantially influence the isotope signatures of N. ovata. These results indicate that rhizoctonia fungi played the major functional role in C and nutrient supply and that ectomycorrhizal fungi did not substantially contribute to the carbon budget of the plants. Read the free Plain Language Summary for this article on the Journal blog.

Mycorrhizal fungi form ubiquitous symbiotic associations with almost all land plants and are of key interest to evolutionary biologists and ecologists because this ancient symbiosis was essential for the colonization of land by plants, a major turning point in the evolutionary history of the earth, and the subsequent development and functioning of the terrestrial ecosystems. Within the orchid family (Orchidaceae), plants establish unique interactions with specific orchid mycorrhizal fungi. These fungal symbionts are essential for the development of orchids as they provide carbon and soil nutrients to germinating orchid seeds and the nutritional supply continues for adult orchids to different degrees. Fueled by the development of DNA sequencing techniques, the diversity of mycorrhizal and other root-associated fungi in orchid roots has been extensively reported in evolutionary and ecophysiological studies. However, the full taxonomic range of orchid-associated fungi remains to be investigated in a broad phylogenetic framework, hampering a further understanding of the evolution and ecological adaptation of orchid mycorrhizal interactions. In this study, we used the most complete DNA dataset to date to map the phylogenetic distribution and ecological lifestyles of root-associated fungi in Orchidaceae by phylogenetic reconstructions at the fungal order level. We found that a broad taxonomic range of fungi (clustered into 1898 operational taxonomic units) resided in orchid roots, belonging to at least 150 families in 28 orders in Basidiomycota and Ascomycota. These fungi were assigned to diverse ecological lifestyles including typical orchid mycorrhizal fungi ("rhizoctonia"), ectomycorrhizal fungi, wood- or litter-decaying saprotrophic fungi, and other endophytes/pathogens/saprotrophs. This overview reveals that among the four different mycorrhizal types, the orchid mycorrhizal symbiosis probably involves the highest diversity of fungal taxa. We hope that our newly reconstructed phylogenetic framework of orchid-associated fungi and the assessment of their potential mycorrhizal status will benefit future ecological and evolutionary studies on orchid-fungal interactions. ### Competing Interest Statement The authors have declared no competing interest.

28 Mycorrhizal fungi form ubiquitous symbiotic associations with almost all land plants and are of key 29 interest to evolutionary biologists and ecologists because this ancient symbiosis was essential for the 30 colonization of land by plants – a major turning point in the evolutionary history of the earth – and the 31 subsequent development and functioning of the terrestrial ecosystems. Within the orchid family 32 (Orchidaceae), plants establish unique interactions with specific orchid mycorrhizal fungi. These fungal 33 symbionts are essential for the development of orchids as they provide carbon and soil nutrients to 34 germinating orchid seeds and the nutritional supply continues for adult orchids to different degrees. 35 Fueled by the development of DNA sequencing techniques, the diversity of mycorrhizal and other root- 36 associated fungi in orchid roots has been extensively reported in evolutionary and ecophysiological 37 studies. However, the full taxonomic range of orchid-associated fungi remains to be investigated in a 38 broad phylogenetic framework, hampering a further understanding of the evolution and ecological 39 adaptation of orchid mycorrhizal interactions. In this study, we used the most complete DNA dataset to 40 date to map the phylogenetic distribution and ecological lifestyles of root-associated fungi in 41 Orchidaceae by phylogenetic reconstructions at the fungal order level. We found that a broad 42 taxonomic range of fungi (clustered into 1898 operational taxonomic units) resided in orchid roots, 43 belonging to at least 150 families in 28 orders in Basidiomycota and Ascomycota . These fungi were 44 assigned to diverse ecological lifestyles including typical orchid mycorrhizal fungi (‘rhizoctonia’), 45 ectomycorrhizal fungi, wood-or litter-decaying saprotrophic fungi, and other 46 endophytes/pathogens/saprotrophs. This overview reveals that among the four different mycorrhizal 47 types, the orchid mycorrhizal symbiosis probably involves the highest diversity of fungal taxa. We 48 hope that our newly reconstructed phylogenetic framework of orchid-associated fungi and the 49 assessment of their potential mycorrhizal status will benefit future ecological and evolutionary studies 50 on orchid-fungal interactions.

Mycorrhizal fungi are central to the biology of land plants. However, to what extent mycorrhizal shifts - broad evolutionary transitions in root-associated fungal symbionts - are related to changes in plant trophic modes remains poorly understood. We built a comprehensive DNA dataset of Orchidaceae fungal symbionts and a dated plant molecular phylogeny to test the hypothesis that shifts in orchid trophic modes follow a stepwise pattern, from autotrophy over partial mycoheterotrophy (mixotrophy) to full mycoheterotrophy, and that these shifts are accompanied by switches in fungal symbionts. We estimate that at least 17 independent shifts from autotrophy towards full mycoheterotrophy occurred in orchids, mostly through an intermediate state of partial mycoheterotrophy. A wide range of fungal partners was inferred to occur in the roots of the common ancestor of this family, including 'rhizoctonias', ectomycorrhizal, and wood- or litter-decaying saprotrophic fungi. Phylogenetic hypothesis tests further show that associations with ectomycorrhizal or saprotrophic fungi were most likely a prerequisite for evolutionary shifts towards full mycoheterotrophy. We show that shifts in trophic mode often coincided with switches in fungal symbionts, suggesting that the loss of photosynthesis selects for different fungal communities in orchids. We conclude that changes in symbiotic associations and ecophysiological traits are tightly correlated throughout the diversification of orchids.

Background The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation . This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. Results In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh -gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. Conclusions Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae.

We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera.

采用典型样地法,对比研究重、中和轻3种强度人为干扰对谢家山润楠(Machilus nanmu)次生林群落结构和物种多样性的影响,采用物种丰富度指数(D)、Simpson优势度指数(H')、Shannon-Wienner多样性指数(H)和均匀度指数(Jsw)来综合衡量群落的物种多样性水平.结果表明:(1)重度干扰群落各层次物种数最少.(2)不同强度人为干扰下润楠次生林的群落结构不同,轻度干扰群落中,在径级Ⅱ[4.0 cm≤胸径(dbh)＜8.0 cm]出现数量峰值(74株);中度干扰群落中,在径级Ⅲ(8.0 cm≤db,h＜12.0 cm)出现数量峰值(62株);重度干扰群落中,群落结构不稳定,在径级Ⅳ(12.0 cm≤db,h＜16.0 em)出现数量峰值(66株).(3)随着干扰强度的增加,重要值集中在润楠、黄连木(Pistacia chinensis和紫苏(Perilla frutescens)等少数物种上.(4)随着干扰强度的加强,灌木层和草本层物种多样性指数均先增加后减小,中度干扰群落灌木层和草本层物种多样性指数明显提高;乔木层各多样性指数均呈下降趋势.

为研究人工林群落的边缘效应特征,本文以川西周公山森林公园的柳杉(Cryptomeria fortunei)人工林破碎化大斑块为对象,以植株平均胸径、平均高度、平均密度、丰富度指数(D)和Shannon-Wiener指数(H)来综合衡量边缘效应深度.在实地踏查的基础上,从林缘向林内(梯度1至梯度5)设置5条样带(宽度为10 m),在每条样带中设置4个10m×10m的小样方进行调查.结果表明:(1)从物种组成上看,在总面积为2,000m2的20个小样方中共记录到111个物种,隶属于54科96属,物种数从林缘至林内递减.(2)从群落结构上看,乔木层的平均胸径从林缘至林内呈减小趋势,平均密度则相反,平均高度无显著变化;灌木层的平均密度从林缘向林内减小,平均高度无显著变化;草本层的平均密度和平均高度均呈减小趋势.(3)从物种多样性上看,总体上各层次的丰富度指数和Shannon-Wiener指数均从林缘向林内呈减小趋势,其中灌木层和草本层的变化趋势最明显;同时,林内各梯度与梯度1(林缘)的共有种和相似性系数从林缘向林内递减.(4)分析各项群落特征发现,平均高度、平均密度和相似性系数的数值在梯度2向梯度3过渡时的起伏变化最明显,推断本研究中柳杉人工林斑块的边缘深度可达林内20 m.

In order to make a thorough inquiry in effects of human disturbance on herbaceous plant community,an inves-tigation has been conducted along Qingyijiang River riparian zone,Ya’an City,Sichuan Province by using the typical sam-pling method.The species Richness index D ,Shannon-Wienner index H ,Simpson index H′and Pielou index J sw were a-dopted to make evaluations on the level of species diversity on herbaceous plant community.There are three kinds of sample areas under human disturbances of three different intensities in the investigated zone:flood lands under slight dis-turbance,mow grasslands under medium disturbance,and abandoned farmlands under severe disturbance.The results showed that sixty-four plant species that belong to 26 families and 53 genera were found in the three kinds of studied are-as.Species richness significantly decreased with the increment of disturbance intensity.By analyzing the important val-ues,it was discovered that under disturbances of all levels of intensities,the main bodies of the communities are composed of the species which belong to Compositae,Gramineae,Leguminosae,Polygonaceae and Umbelliferae.However,there was no obvious main edificatory in the communities under disturbances of different levels of intensities,since the impor-tant values of each species has no significant difference,indicating the intenses of interspecific competitions.The results indicated that the numbers of the species with niche overlap values above 0.5 in communities under light disturbances, medium disturbances and severe disturbances respectively accounted for 95.0%,85.4% and 74.2% of the total species numbers.S?rensen’s similarity coefficient (S S )between communities under disturbances of different levels of intensities were different.S?rensen’s similarity coefficient (S S )between communities under slight and medium disturbances,medi-um and severe disturbances,and slight and severe disturbances were 0.733,0.719 and 0.625,respectively.Species richness index D and Shannon-Wiener index H decreased with the increment of the human disturbance intensity,the sequences of them were slight disturbance>medium disturbance>severe disturbance,and the difference among disturbance intensities were significant.However,there was no significant differences of Simpson index H′ and Pielou index J sw among sample areas.