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21 results for “Shorea”
Herbarium specimen image of Shorea Roxb. ex C.F.Gaertn., part of the collection of National Museum of Natural History, Paris
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.
Growth traits of a tropical timber species at Southeast Asia, Shorea macrophylla, and scripts for genome wide association study and genomic prediction
<p><em><span>Shorea macrophylla</span></em><span> is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to <em>S. macrophylla</em>. To build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of <em>S. macrophylla</em> in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for breast height and total height in the 7th year from planting (D7 and H7). These traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 12 methods with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability (PA) for D7 and H7 and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high PA for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. For almost all methods and both traits, PA was higher when SNPs were selected based on their GWAS P-values than when using the full set of SNPs. These results suggest that GS with GWAS-based SNP selection could be used in <em>S. macrophylla </em>breeding to improve initial growth and reduce genotyping costs for next generation seedlings.</span></p>
FIG. 11. — Russula shoreae D.Chakr., A.Ghosh, K in Three new species of genus Russula Pers. from Sal dominated forests of tropical India based on morphotaxonomy and multigene phylogenetic analysis
FIG. 11. — Russula shoreae D.Chakr., A.Ghosh, K.Das & Buyck, sp. nov. (from holotype): A-C, fresh and dissected basidiomata in the field and basecamp; D, E, transverse section through pileipellis showing elements; F, transverse section through lamellae showing basidia; G, H, transverse section through lamellae showing hymenial cystidia near the lamellae edges; I-M, transverse section through lamellae showing hymenial cystidia near the lamellae sides. Scale bars: A, B, 20 mm; D, 20 μm; E-M, 10 μm.
FIG. 12. — Russula shoreae D.Chakr., A.Ghosh, K in Three new species of genus Russula Pers. from Sal dominated forests of tropical India based on morphotaxonomy and multigene phylogenetic analysis
FIG. 12. — Russula shoreae D.Chakr., A.Ghosh, K.Das & Buyck, sp. nov. (from holotype): A, basidiospore; B, elements of the pileipellis near the pileus margin: hyphal terminations and pileocystidia; C, hymenial cystidia near the lamellae sides; D, basidia; E, hymenial cystidia near the lamellae edges; F, elements of the pileipellis near the pileus centre: hyphal terminations and pileocystidia. Scale bars: 10 µm.
Growth traits of a tropical timber species at Southeast Asia, Shorea macrophylla, and scripts for genome wide association study and genomic prediction
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Characterization of leaf transcriptome in a tropical tree species, Shorea curtisii, over a flowering season
<p><span>General flowering (GF) is a synchronous flowering event in the Southeast Asian tropical rainforests that occurs at irregular intervals of multiple years. The unpredictable intervals of GF raise conservation concerns for these under-researched forests with rich economically and ecologically important species. In this study, the leaf transcriptome of a GF species, <em>Shorea</em> <em>curtisii</em> obtained from three time points – before and after floral initiation, and post flowering stage – was sequenced. We assembled 243,759,478 sequencing reads into 39,943 non-redundant unigenes including 677 putative homologs of <em>Arabidopsis</em> <em>thaliana</em> flowering-related genes. Differential expression analysis conducted on pairwise comparisons of the time points identified 930 differentially expressed unigenes, which includes 17 flowering-related homologs. The differential expression of unigenes with significant enrichments of functions related to drought corroborated the involvement of drought as an environmental cue for GF. The outcomes of this study offer an insight into the conservation of floral regulatory genes and pathways in Shorea and could be used as a model to better understand the floral initiation cues and regulation of GF trees.</span></p>
Characterization of leaf transcriptome in a tropical tree species, Shorea curtisii, over a flowering season
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Data from: Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation
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Data from: Species-specific flowering cues among general flowering Shorea species at the Pasoh Research Forest, Malaysia
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Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia
Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the southwestern part of Borneo genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28 to 0.09 million years before present, and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
Data from: Effects of Pleistocene climate change on genetic structure and diversity of Shorea macrophylla in Kalimantan rainforest
The island of Borneo is the diversity center of the Dipterocarpaceae, the most important family of tropical rainforest trees in Southeast Asia. However, changes in land use and climate have affected dipterocarp distributions on the island, raising concerns about the vulnerability (inter alia) of the endemic riparian species Shorea macrophylla. Thus, to aid conservation efforts we have investigated the genetic diversity, structure and demographic history of S. macrophylla. The species' genetic diversity and structure in Kalimantan (part of Indonesia, covering 75% of the island) was explored by examining genotypes of 377 individuals representing 13 populations in three regions (Northeast, Central and West Kalimantan) using 14 newly developed microsatellite loci. Higher genetic diversity was found, at all loci, in samples from Northeast Kalimantan than in samples from the other regions. Moderate genetic differentiation between populations was detected (FST: 0.093). Bayesian clustering, principal coordinate, and neighbor joining tree analysis of the population structure consistently identified two genetically distinct groups, one in the Northeast and the other in the Central and West regions. The higher diversity of the diverged populations in Northeast Kalimantan indicates that the region may have hosted rainforest refugia during the ice age. Accordingly, analysis using DIY ABC software indicated that the Northeast and Central-West Kalimantan groups diverged 194 000 years ago. We conclude that global climate change during the Pleistocene strongly influenced the genetic diversity and structure of S. macrophylla populations in Kalimantan.
FIGURE 2 in A new edible species of Lactifluus (Russulaceae) from Shorea robusta dominated forests in tropical India
FIGURE 2. Lactifluus tropicalis (CAL 1873, holotype). a–c. Fresh and dissected basidiomata in the field and basecamp, d. Transverse section through pileipellis showing elements, e. Transverse section through lamellae showing basidia, f–j. Transverse section through lamellae showing pleuropseudocystidia, k & l. SEM micrograph of basidiospores. Scale bars: d= 20 μm, e−j= 10 μm, k & l= 2 μm.
FIGURE 1 in A new edible species of Lactifluus (Russulaceae) from Shorea robusta dominated forests in tropical India
FIGURE 1. Phylogram of Lactifluus tropicalis and their allied species based on a Maximum Likelihood and Bayesian analyses of nrITS, nrLSU and rpb2 gene sequences. Support values in either the Maximum Likelihood [ML Bootstrap percentage (MLBs)] or Bayesian [Posterior probabilities values (BPP)] analyses are indicated. MLBs ≥70% are shown on the left of "/" and BPP ≥0.95 are shown on the right above or below the branches at nodes. Lactifluus tropicalis is placed in bold red font to highlight its phylogenetic positions in the tree.
FIGURE 3 in A new edible species of Lactifluus (Russulaceae) from Shorea robusta dominated forests in tropical India
FIGURE 3. Lactifluus tropicalis (CAL 1873, holotype). a. Pleuropseudocystidia, b. Basidiospores, c. Basidia, d. Pileipellis. Scale bars: a, c, d= 10 µm, b= 2 µm.
FIGURE 1. Shorea tumbuggaia. A in Lectotypification of the names Shorea tumbuggaia and S. penicillata (Dipterocarpaceae)
FIGURE 1. Shorea tumbuggaia. A. Habit; B. Bark; C. Close-up of leaves; D. Close-up of flower; E. Branchlet with fruits; F. Close-up of fruits.
FIGURE 3 in Lectotypification of the names Shorea tumbuggaia and S. penicillata (Dipterocarpaceae)
FIGURE 3. Lectotype of Shorea penicillata Candolle (P06717479, © Muséum National d'Histoire Naturelle, Paris).
FIGURE 2 in Lectotypification of the names Shorea tumbuggaia and S. penicillata (Dipterocarpaceae)
FIGURE 2. Lectotype of Shorea tumbuggaia Roxburgh (Roxburgh's Icon no. 1566, Image © The Trustees of the Royal Botanic Gardens, Kew).
Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia
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Data from: Mixed mating system are regulated by fecundity in Shorea curtisii (Dipterocarpaceae) as revealed by comparison under different pollen limited conditions
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Data from: Effects of Pleistocene climate change on genetic structure and diversity of Shorea macrophylla in Kalimantan rainforest
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International Brain Laboratory public data
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OpenNeuro
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