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Datasets for manuscipt Use of Weighted Voronoi diagram for forest thinning proposal and skidding trail layout for teak plantation in Thailand
<p>Project package used in manuscript entitled: Use of Weighted Voronoi diagram for forest thinning proposal and skidding trail layout for teak plantation in Thailand. Project package can be open in ArcGIS Pro and contains raster datasets and shapefiles. Zip file contains unpacked package into the folder with spatial data and project file (APRX). </p>
Data from: Shifting agriculture supports more tropical forest birds than oil palm or teak plantations in Mizoram, northeast India
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Tectona grandis: Narrow Genetic Base? A New Perspective on the Genetic Variability of Teak
Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its origin centers and little is known about the genetic origin and genetic variability. This study aimed to investigate the genetic diversity and population structure existing in a teak germplasm bank collection in Brazil. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 8x of coverage, the sequencing were aligned using the genome at NCBI, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four subpopulations with genetic variability between and within the subpopulations, so this study made it possible to confirm the existence of genetic variability in teak, contrary to what was expected.
Tectona grandis: Narrow Genetic Base? A New Perspective on the Genetic Variability of Teak
Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its origin centers and little is known about the genetic origin and genetic variability. This study aimed to investigate the genetic diversity and population structure existing in a teak germplasm bank collection in Brazil. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 8x of coverage, the sequencing were aligned using the genome at NCBI, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four subpopulations with genetic variability between and within the subpopulations, so this study made it possible to confirm the existence of genetic variability in teak, contrary to what was expected.
Tectona grandis: Narrow Genetic Base? A New Perspective on the Genetic Variability of Teak
Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its origin centers and little is known about the genetic origin and genetic variability. This study aimed to investigate the genetic diversity and population structure existing in a teak germplasm bank collection in Brazil. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 8x of coverage, the sequencing were aligned using the genome at NCBI, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four subpopulations with genetic variability between and within the subpopulations, so this study made it possible to confirm the existence of genetic variability in teak, contrary to what was expected.
De novo genome assembly of Tectona grandis (Teak) with 2993 scaffolds
<p>Teak (<em>Tectona grandis</em> L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed <em>in silico</em> polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus <em>Tectona</em> within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the <em>Tectona</em> genus to be around 21.4508 million years ago.</p>
Data from: Genetic resources of teak (Tectona grandis Linn. f.) – strong genetic structure among natural populations
Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern of genetic diversity supports the hypothesis that teak has its centre of origin in India, from where it spread eastwards. The analysis of molecular variance (AMOVA) gave an overall highly significant F st value of 0.227—population pairwise F st values were in the range 0.01–0.48. Applying the G″st differentiation parameter, the estimated overall differentiation was 0.632, implying a strong genetic structure among populations. A neighbour-joining (NJ) tree, using the pairwise population matrix of G″st values as input, contained three distinct groups: (1) the eight provenances from Thailand and Laos, (2) the Indian provenances from the dry interior and the moist west coast and (3) the provenances from northern Myanmar. The provenances from southern Myanmar were placed close to the root of the tree together with the three provenances from the semi-moist east coast of India. A Bayesian cluster analysis using the STRUCTURE software gave very similar results, with three main clusters, each containing two sub-clusters, while Bayesian cluster analysis in the Geneland software, exploiting the spatial coordinates of the provenances, resulted in five clusters in accordance with the former results. The implications of the findings for conservation and use of genetic resources of the species are discussed.
Data from: Understory diversity and composition after planting of teak and mahogany in Yogyakarta, Indonesia
<p>Forest rehabilitation is when a desired tree species is planted in degraded forests or lands. Rehabilitation by planting a single tree species is a common way to restore exploited forests to maintain ecological processes. We compared woody and herbaceous understory vegetation between forests rehabilitated by mahogany (N = 12) or teak (N = 12) planted from 1941 until 2003 in Yogyakarta, Indonesia. Understory vegetation of these areas were compared with that of three native forests. Species richness, species diversity, density of plants and proportion of native plants did not differ between the rehabilitated areas and the native forest. Recently rehabilitated areas were different from the native forests while 41-74 years after rehabilitation, characteristics of understory vegetation approached those of native forest. We described species composition using ordination, and found it to differ between areas rehabilitated with teak and with mahogany and, particularly, between the rehabilitated areas and the native forests. Time since rehabilitation and tree species planted were important for the species composition of understory vegetation. We conclude that the selection of species for rehabilitation and letting rehabilitated areas mature are important for understory development and species diversity.</p>
FIGURE 8 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 8. Pseudofusicoccum adansoniae (MFLU 15-0731) a, b. Leaf spot on T. grandis with associated conidiomata. c. Section through conidioma. d–f. Conidia attached to conidiogenous cells. g–o. Conidia. Scale bars: a=1000 μm. b=300 μm.c=30 μm. d=20 μm. e, g–o=10 μm. f=5 μm.
FIGURE 6 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 6. Lasiodiplodia brasiliense (MFLUCC 11-0414) a. Conidia formed on dead branches of Tectona grandis after incubation in a moist chamber for10 days. b. Colony on MEA after 1 week, and inset a conidioma on the agar surface after 1 month. c. Immature conidia attached to conidiogenous cells with paraphyses. d-f. Immature conidia attached to conidiogenous cells. g. Paraphyses. h. Immature conidia. i–k. Mature conidia. Note: c stained with lactophenol cotton blue. c–i, k. Morphology in culture. j morphology on host. Scale bars: a=100 μm. b=300 μm. c–k=10 μm.
FIGURE 7 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 7. Lasiodiplodia pseudotheobromae (MFLU 14-0270) a, b. Conidiomata and conidia on surface of dead twig of Tectona grandis. c. Section through conidioma. d. Conidioma wall. e. Conidia attached to conidiogenous cells with paraphyses. f, g. Immature conidia. h–j. Mature conidia in two different focal planes showing longitudinal striations. k, l. Germinated mature conidia. Note e, g stained with lacto-phenol cotton blue. Scale bars: a=300 μm. b=200 μm. c=100 μm. d, f=20 μm. e, g–l=10 μm.
FIGURE 5 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 5. Dothiorella tectonae (MFLU 14-0272, holotype) a. Conidiomata on dead branch of T. grandis. b. Section through conidioma with conidia becoming dark and aseptate or 1–septate while still attached to conidiogenous cells. c. Conidioma wall. d–e. Conidia attached to conidiogenous cells. f–j. Mature conidia (arrow showing short raised irregular striations on conidia surface). k. Spermatogenous cells and spermatia. l. Germinated mature conidium. Note d, e. stained with lactophenol cotton blue. Scale bars: a=300 μm. b=50 μm. c, e=10 μm. d, f–l=5 μm.
FIGURE 4 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 4. One of 4 most parsimonious trees (CI= 0.912, HI= 0.088, RI= 0.927, RC= 0.845) resulting from combined ITS, TEF1-α and BT analysis for nine taxa in Sphaeropsis species. The tree is rooted to Barriopsis fusca. Maximum parsimony bootstrap values ≥70%, Bayesian posterior probabilities ≥ 0.90 are given at the nodes (MPBS/PP). Type isolates are marked with T. Isolates from this study are in bold.
FIGURE 1 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 1. Phylogenetic trees resulting from individual analyses of each dataset and combined dataset. a. One of>200 most parsimonious trees (CI= 0.622, HI= 0.378, RI= 0.863, RC= 0.537) resulting from ITS analysis for 40 taxa in Dothiorella species, b. Bayesian analysis tree resulting from ITS analysis, c. One of>200 most parsimonious trees (CI= 0.635, HI= 0.365, RI= 0.867, RC= 0.550) resulting from TEF1-α analysis for 39 taxa, d. One of 24 most parsimonious trees (CI= 0.750, HI= 0.250, RI= 0.891, RC= 0.668) resulting from BT analysis for 29 taxa, e. One of 63 most parsimonious trees (CI= 0.642, HI= 0.358, RI= 0.863, RC= 0.554) resulting from combined ITS, TEF1-α and BT analysis for 40 taxa. The tree is rooted to two isolates of Spencermartinsia viticola. Maximum parsimony bootstrap values ≥50%, Bayesian posterior probabilities ≥ 0.90 (MPBS/PP) are given at the nodes. Type isolates are marked with T. Isolates from this study are in blue bold.
FIGURE 2 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 2. One of 48 most parsimonious trees (CI= 0.674, HI= 0.326, RI= 0.881, RC= 0.594) resulting from a combined ITS, TEF1-α and BT analysis for 56 taxa in Lasiodiplodia species. The tree is rooted to isolates of Diplodia mutila and D. seriata. Maximum parsimony bootstrap values ≥50%, Bayesian posterior probabilities ≥ 0.90 (MPBS/PP) are given at the nodes. Type isolates are marked with T. Isolates from this study are in bold.
FIGURE 3 in Botryosphaeriaceae associated with Tectona grandis (teak) in Northern Thailand
FIGURE 3. One of 12 most parsimonious trees (CI= 0.909, HI= 0.091, RI= 0.943, RC= 0.857) resulting from combined ITS and TEF1- α analysis for 20 taxa in Pseudofusicoccum species. The tree is rooted to two isolates of Neofusicoccum parvum. Maximum parsimony bootstrap values ≥50%, Bayesian posterior probabilities ≥ 0.90 (MPBS/PP) are given at the nodes. Type isolates are marked with T. Isolates from this study are in bold.
FIGURE 2 in Barriopsis tectonae sp. nov. a new species of Botryosphaeriaceae from Tectona grandis (teak) in Thailand
FIGURE 2. The most parsimonious trees (tree length= 1042, CI= 0.651, HI= 0.349, RI= 0.854, RC= 0.556) resulting from a combined ITS, TEF1-α and BT analysis for 38 taxa in the Botryosphaeriaceae. Maximum parsimony bootstrap values ≥70% are given above the nodes. Bayesian posterior probabilities ≥ 0.95 are given below the nodes. The tree was rooted to Pseudofusicoccum stromaticum.
FIGURE 1 in Barriopsis tectonae sp. nov. a new species of Botryosphaeriaceae from Tectona grandis (teak) in Thailand
FIGURE 1. Barriopsis tectonae (MFLU 14-0024, holotype) A. Ascostromata on host. B. Ascostromata cut through horizontally showing the white contents with dark spots. C–D. Section through ascoma on host. E. Papilla with periphyses. F. Peridium. G. Pseudoparaphyses. H. Immature ascus. I–J. Immature ascus with hyaline ascospores, mature asci with brown ascospores. K, M. Mature ascospore/s without terminal apiculi. L. Immature ascopsore without longitudinal striations. N. Germinated ascospore. O. Immature conidium. P. Mature conidium with two septa. Q, R. Mature conidia with longitudinal striations. Scale bars: A, B = 500 µm, C = 100 µm, D, K = 50 µm, E, H–J, N = 20 µm, F, G, L, M, O–R = 10 µm.
Fig. 1. A in Teak,Tectona grandisL.F. (Lamiaceae), as a New Host Plant ofSteirastoma breve(Sulzer, 1776) (Coleoptera: Cerambycidae)
Fig. 1. A) Dead Tectona grandis trees 3.5 years after planting, B) Frass ejected from oval holes, C) Steirastoma breve, adult male, D) Larva of S. breve collected from teak, E) Injury to teak wood caused by larvae.
Data from: Genetic resources of teak (Tectona grandis Linn. f.) – strong genetic structure among natural populations
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