cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mt24h/6
title: No.3 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/7
title: No.4 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/8
title: No.4 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/9
title: No.5 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.n5509/1
title: Chukchi Sea Polar Bear Locations (2008-2013)

description: These data are the locations (latitude and longitude) of polar bears in the Chukchi Sea that were used in the analysis by Rode et al.  The data include the date and time of the location, the unique identifier of the bear the locations are from, and the accuracy classification of the location.  Location accuracy is based on Argos error classes (3,2,1,0,A,B).  If a location was obtained from GPS, its accuracy is labeled as 'GPS'.
DOI: 10.5061/dryad.ng785/5
title: discrimination-data-exp1

description: Data from the discrimination learning in Experiment 1.
DOI: 10.5061/dryad.ng785/6
title: generalization-data-exp1

description: Data from the generalization test in Experiment 1.
DOI: 10.5061/dryad.p760b/1
title: A_assembly_RABT

description: The reference annotation based transcript (RABT) assembly of individual A transcriptome
DOI: 10.5061/dryad.p760b/2
title: B_assembly_RABT

description: The reference annotation based transcript (RABT) assembly of individual B transcriptome
DOI: 10.5061/dryad.p760b/3
title: C_assembly_RABT

description: The reference annotation based transcript (RABT) assembly of individual C transcriptome
DOI: 10.5061/dryad.qg7p3/1
title: latitude, herbivore attack, plant defenses, and climatic data

description: Ruellia nudiflora population-level values for defenses, herbivore attack, and parasitoid attack. Variables are ordered and labeled in the following way: "population" = plant population name; "latitude" = decimal degrees latitude for each population ; "pctemperature" = z-score values from first principal component of PCA analysis of temperature-related variables (from WorldClim); "pcprecipitation" = z-score values from first principal component of PCA analysis of precipitation-related variables (from WorldClim); "seedphenolics" = concentration of phenolic compounds in seeds; "leafphenolics" = concentration of phenolic compounds in leaves; "fruitattack" = mean proportion of attacked fruits by seed herbivore; "parasitoidattack" = mean proportion of seed herbivores parasitized; "leafdamage" = mean leaf damage score; "trichomedensity" = mean leaf trichome density.
DOI: 10.5061/dryad.rr85h/1
title: Supp Fig. 1 Adelonema ITS ML

description: The maximum likelihood tree of 116 taxa based on the ITS1, ITS2, and the 5.8S regions of the nuclear rRNA gene. Bootstrap (BS) values are shown above/below next to each internal branch.
DOI: 10.5061/dryad.rr85h/2
title: Supp Fig. 2 Adelonema matK ML

description: The maximum likelihood tree of 55 taxa (Adelonema, Homalomena, Philodendron and outgroup) based on matK and partial trnK (matK) plastid region. Bootstrap (BS) values are shown above/below/next to the branch.
DOI: 10.5061/dryad.rr85h/3
title: Supp Fig. 3 Adelonema combined ML

description: The maximum likelihood tree of 38 taxa (Adelonema, Homalomena, Philodendron and outgroup) based on combined ITS and matK regions. Bootstrap (BS) values are shown above/below/next to the branch.
DOI: 10.5061/dryad.sr61r/1
title: RCAsimulation

description: RCAsimulation.zip contains the simulation code (MATLAB) used in Kopps et al. 2015 and a manual on how to run the simulation.
DOI: 10.5061/dryad.td570/2
title: Appendix S1

description: Excel file containing all data on pterosaur completeness, proxies, groupings, and model outputs.
DOI: 10.7267/n94q7rw1
title: Household Survey Data 2010: Dams and Population Displacement on China’s Upper Mekong River

description: This is the data set used for the analysis in the paper "Dams and Population Displacement on China’s Upper Mekong River: Implications for Social Capital and Social-Ecological Resilience." In 2010, in collaboration with Chinese colleagues, we administered a household survey questionnaire to 729 households in more than 30 villages across Fengqing, Yun, and Lancang counties in Yunnan Province, China. Because of our specific interest in agriculture and social capital for this paper, we restricted the sample in our analysis to include only those households who reported participating in farming activities during the previous 12 months, removing 56 households. We also removed an additional 201 households who had not participated in at least some labor exchange during the previous 12 months, on the assumption that their farming practices were different, less reliant on labor exchange. Our final sample thus contained 472 households in the vicinity of four dam sites (Manwan=143, Dachaoshan=106, Xiaowan=150, Nuozhadu=73). The complete data set (Brown and Tilt 2010) includes modules on demographic, social, cultural and economic conditions; agricultural production; and other variables. However, this restricted data set includes only information on our independent variables (resettlement status, dam site), dependent variables (exchange of financial resources -- both number of households and amounts; and exchange of farm labor -- both number of households and amounts), and control variables (land holdings, ethnicity, and income).
DOI: 10.5061/dryad.266k4/1
title: plink files for cornell canine dataset

description: ID and sex information for each dog
DOI: 10.5061/dryad.2pm6f/1
title: Hinrichsen et al_Royal Society Open Science_Bongogrid_Fig1

description: This file contains the geographic coordinates of the specific locations where plankton samples (including cod eggs) for analyses in this manuscript were collected (see read me file for details).
DOI: 10.5061/dryad.2pm6f/2
title: Hinrichsen et al_Royal Society Open Science_Baltic cod spawning stock size and age composition_Fig2

description: This worksheet summarizes the Baltic cod stock characteristics (number per age class, mean weight, spawning stock biomass, mean age) for the time-series 1966-2011(see read me file for details).
DOI: 10.5061/dryad.2pm6f/3
title: Hinrichsen et al_Royal Society Open Science_Egg survival_Fig3

description: This worksheet contains the mean hydrographic conditions and resulting egg survival for the period 1951-2010 for Bornholm Basin (see read me file for details).
DOI: 10.5061/dryad.2pm6f/4
title: Hinrichsen et al_Royal Society Open Science_cod egg diameter and water density correlation_Fig4

description: This worksheet lists the mean measured diameter of cod eggs derived from multinet hauls across Bornholm Basin and the correlated water density in which they were caught (see read me file for details).
DOI: 10.5061/dryad.2pm6f/5
title: Hinrichsen et al_Royal Society Open Science_O2 and survival on water density levels BB_Fig5

description: This file contains six worksheets, each with a datasets on O2 content and the corresponding oxygen related survival of cod eggs on the positional grid of the Bornholm Basin (1 dataset for each combination of 3 different water density levels x 2 timepoints) (see read me file for details).
DOI: 10.5061/dryad.2pm6f/6
title: Hinrichsen et al_Royal Society Open Science_spawning area extensions and corresponding egg survival_Fig6 and 7

description: This worksheet contains data for spawning area extensions, and mean oxygen content and oxygen related cod egg survival for each area, for different water density levels and months for the time period 1993-2010 (see read me file for details).
DOI: 10.5061/dryad.2pm6f/7
title: Hinrichsen et al_Royal Society Open Science_Stock-recruitment_Fig8

description: This worksheet contains the data underlying the stock-recruitment plots in this manuscript for the years 1966-2012 (see read me file for details).
DOI: 10.5061/dryad.31733/10
title: Pa-Ndjo11-R11T19_R1R2.fastq

description: Podococcus barteri Pb-Ndjo11 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/11
title: Pb-Aloum8-R11T73_R1R2.fastq

description: Podococcus barteri Pb-Aloum8 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/12
title: Pb-Campo1-R11T81_R1R2.fastq

description: Podococcus barteri Pb-Campo1 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/13
title: Pb-Kola5-R11T54_R1R2.fastq

description: Podococcus barteri Pb-Kola5 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/14
title: Pb-Oyem-R11T47_R1R2.fastq

description: Podococcus barteri Pb-Oyem sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/15
title: Pb-Podo5-1-R2T53_R1R2.fastq

description: Podococcus barteri Podo 5-1 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/6
title: P458_Run4-TAG-25

description: Dioscorea praehensilis P458 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/7
title: Pa-Mayo9-R11T57_R1R2.fastq

description: Podococcus acaulis Pa-Mayoko9 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/8
title: Pa-Ndjo3-R11T18_R1R2.fastq

description: Podococcus acaulis Pa-Ndjo3 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/9
title: Pa-Ndjo9-R11T16_R1R2.fastq

description: Podococcus acaulis Pa-Ndjo9 sample - Chloroplast enrichment sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.7231d.1
title: Data from: Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders
DOI: 10.5061/dryad.7231d.2/10.2
title: LAGRANGE_tree

description: Pruned tree used for input in LAGRANGE 7 and 2 area range reconstruction
DOI: 10.5061/dryad.7231d.2/11.2
title: Palpimanoidea Morphology + DNA_Bayes

description: Nexus file containing molecular and morphological characters used for MrBayes total evidence phylogenetic analysis, from Wood et al. 2012
DOI: 10.5061/dryad.8661.1
title: Data from: Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms
DOI: 10.5061/dryad.8661.2
title: Data from: Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms
DOI: 10.5061/dryad.8661.2/1.2
title: concatenated 4-gene matrix
DOI: 10.5061/dryad.8bj97/1
title: sequences related to Figures 2, 3 and 6
DOI: 10.5061/dryad.8qk33/1
title: Bristle dataset of D. melanogaster

description: Bristle counts of sternopleurals (SP), ocellar bristles (OC), and orbital bristles (OB) for 61 deficinecy/wild-type genotypes of Drosophila melanogaster.  Each entry represents mean bristle counts at replication vial level.
DOI: 10.5061/dryad.93j174jd.2
title: Data from: New fossil penguins (Aves, Sphenisciformes) from the Oligocene of New Zealand reveal the skeletal plan of stem penguins
DOI: 10.5061/dryad.93j174jd.2/1.2
title: Kairuku JVP Dataset - nexus file

description: Combined phylogenetic dataset for penguin phylogeny. 245 morphological characters, sequence data from RAG-1, cytochrome b, 12SrDNA, 16SrDNA and COI. 58 penguin species, 15 outgroup species. The revised nexus file contains no character scoring changes, but we have added the character descriptions directly to the file to assist those wishing to expand or reuse the matrix.
DOI: 10.5061/dryad.93j174jd.2/2.2
title: Kairuku JVP Dataset - supplementary data

description: Combined phylogenetic dataset for penguin phylogeny. 245 morphological characters, sequence data from RAG-1, cytochrome b, 12SrDNA, 16SrDNA and COI. 58 penguin species, 15 outgroup species. The original character list contained a numbering error, resulting in several characters in the 201-208 range being out of order. The new version of the character list has been corrected to indicate the proper numbering.
DOI: 10.5061/dryad.94t53/1
title: Task-based functional connectivity matrices

description: Task-based functional connectivity matrices, in MATLAB data format (.mat).
DOI: 10.5061/dryad.94t53/2
title: Resting-state functional connectivity matrices

description: Resting-state functional connectivity matrices, in MATLAB data format (.mat).
DOI: 10.5061/dryad.b78fb/1
title: Genotypes (9 microsatellites) and coordinates of individuals (adults, seedlings, seeds) used in the study

description: Column A: Individual ID; Colum B: Country of origin; Colum C: cohort of the individual (adult, seedling, seed); Columns D and E: coordinates of the individuals (degree decimals); Colmums F to W: genotypes of the individuals at the 9 nuclear SSR (23, 4, 3, 18, 14, 6, 17, 7 and 1).
DOI: 10.5061/dryad.dd3ph.1
title: Data from: Breaking and re-making a seed and seed predator interaction in the introduced range of Scotch Broom (Cytisus scoparius) in New Zealand
DOI: 10.5061/dryad.dd3ph.2/5.2
title: beetle size before & after winter

description: Variables: site_code: 3 sites, eb (East Block, Lincoln), pn (Palmerston North), po (Poutu). All three sites were visited in 2007-2008 but only pn was visited in 2010-2011. pre_post: pre, post. Factor with two levels pre and post hibernation size. sex: m=male, f=female. elytra_area: size of beetle elytra in mm2. year: 2008, 2011.
DOI: 10.5061/dryad.dn08t/10
title: MrBayesGeneTrees_OxalisHybSeq

description: Bayesian inference gene trees of 727 low-copy nuclear genes of 25 southern African Oxalis accessions and Oxalis corniculata.
DOI: 10.5061/dryad.dn08t/11
title: RAxMLGeneTrees_OxalisHybSeq

description: Maximum likelihood gene trees of 727 low-copy nuclear genes of southern African Oxalis accessions and Oxalis corniculata.
DOI: 10.5061/dryad.dn08t/12
title: plastome_MrBayesMajorityRuleConsensusTree_OxalisHybSeq

description: Bayesian inference majority rule consensus tree of the plastome of 25 southern African Oxalis accessions and Oxalis latifolia. The alignment was partitioned into protein-, tRNA-, and rRNA-coding as well as intron/spacer (i.e., non-coding) regions.
DOI: 10.5061/dryad.dn08t/13
title: nrDNAcistron_MrBayesMajorityRuleConsensusTree_OxalisHybSeq

description: Bayesian inference majority rule consensus tree of the nrDNA cistron of 25 southern African Oxalis accessions and Oxalis corniculata. The nrDNA alignment was partitioned into 18S, ITS1, 5.8S, ITS2 and 26S.
DOI: 10.5061/dryad.dn08t/14
title: geneious_deNovoAssembly_OxalisHybSeq

description: FASTA output of the de novo assembly of the transcript or genome skim BLAT hits to larger contigs (step 7 of Sondovač)
DOI: 10.5061/dryad.dn08t/15
title: probeSequences_OxalisHybSeq

description: Final low-copy nuclear probe sequences (output of step 11 of Sondovač)
DOI: 10.5061/dryad.dn08t/7
title: MRP_supertree_fromMrBayesGeneTrees_OxalisHybSeq

description: MRP supertree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.dn08t/8
title: MRP_supertree_fromRAxMLGeneTrees_OxalisHybSeq

description: MRP supertree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.dn08t/9
title: concatenatedLCNloci_bootstrapped_RAxML_OxalisHybSeq

description: Bootstrapped maximum likelihood tree based on concatenation of 727 low-copy nuclear genes of 25 southern African Oxalis accessions. Oxalis corniculata was used as outgroup.
DOI: 10.5061/dryad.f6k78/1
title: Observation points for 4 mexican species of Magnolia Section Macrophylla

description: Specimen based georeferenced records for Magnolia nuevoleonensis, Magnolia dealbata, Magnolia vovidesii and Magnolia rzedowskiana. Data stored in ESRI Shapefile (.shp) format, 4 separate layers compressed in single ZIP archive.
DOI: 10.5061/dryad.h6r35.1
title: Data from: Seasonality of precipitation interacts with exotic species to alter composition and phenology of a semi-arid grassland
DOI: 10.5061/dryad.h6r35.2
title: Data from: Seasonality of precipitation interacts with exotic species to alter composition and phenology of a semi-arid grassland
DOI: 10.5061/dryad.h6r35.2/1.2
title: precipitation_experiment_cover_data

description: This data file contains absolute percent cover measurements of vegetation in plots of a precipitation experiment in a mixed-grass prairie in Colorado. Cover measurements were made in April, June, and August 2011-2013. The 'treatment' column heading corresponds to the precipitation treatment received by the plot, ‘winwet’ = winter wet, ‘winwet_sumdry’ = winter wet/summer dry, ‘windry_sumwet’ = winter dry/summer wet, and ‘windry_sumwet’ = winter dry/summer wet. ‘Ex_grass’ = percent cover of exotic grasses, ‘ex_forbs’ = cover of exotic forbs, ‘cool_grass’ = cover of native cool season grasses, ‘warm_grass’ = cover of native warm season grasses, and ‘total_veg’ = cover of all live vegetation.
DOI: 10.5061/dryad.h6r35.2/2.2
title: precipitation_experiment_resources

description: This data file contains measurements of soil resources and plant community characteristics from a precipitation experiment in a mixed-grass prairie in Colorado. All measurements were made from 2011-2013. The 'treatment' column heading corresponds to the precipitation treatment received by the plot; ‘winwet’ = winter wet, ‘winwet_sumdry’ = winter wet/summer dry, ‘windry_sumwet’ = winter dry/summer wet, and ‘windry_sumwet’ = winter dry/summer wet. ‘Spring_nitrogen’ = total nitrogen extracted from resin bags buried in plots at 5 cm depth from April-May (units are µg N / gram resin). ‘summer_nitrogen’ = total nitrogen extracted from resin bags from June- September, ‘winter_nitrogen’ = total nitrogen extracted from resin bags from October-March. Units for aboveground biomass are g/m2. ‘VWC’ = soil volumetric water content (%) from 0 – 12 cm depth. ‘Diversity’ = Shannon-Weiner diversity index. ‘April_B_tectorum’ = % cover of Bromus tectorum in plots in April.
DOI: 10.5061/dryad.m0420/2
title: Script for all analyses conducted in R. This includes migration matrices, forward projected matrices, and subsampling code
DOI: 10.5061/dryad.mt24h/11
title: No.6 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/12
title: No.6 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/13
title: No.7 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/14
title: No.7 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/15
title: No.8 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/16
title: No.8 TB patient's microbiome (Group B)
DOI: 10.5061/dryad.mt24h/17
title: No.9 TB patient's microbiome (Group A)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.mt24h/18
title: No.9 TB patient's microbiome (Group B)

description: Group A means the microbiome from lesion-free lung lobe; Group B means the microbiome from lesion-forming lung lobe; Group H means the microbiome from healthy individuals.
DOI: 10.5061/dryad.ng785/7
title: salience-data-exp2

description: Data from the salience test in Experiment 2.
DOI: 10.5061/dryad.p760b/10
title: Transcriptome_comparisons_among_tissues

description: The unique annotated accessions from each tissue type for comparison
DOI: 10.5061/dryad.p760b/11
title: FPKM_Super_Transcriptome

description: The FPKM value for each gene locus from the 'Super' transcriptome based on the RABT method
DOI: 10.5061/dryad.p760b/4
title: D_assembly_RABT

description: The reference annotation based transcript (RABT) assembly of individual D transcriptome
DOI: 10.5061/dryad.p760b/5
title: Super_assembly_RABT

description: The reference annotation based transcript (RABT) assembly of pooled libraries (Super transcriptome)
DOI: 10.5061/dryad.p760b/6
title: Perl Script

description: This Perl script enables you to extract the longest open reading frame (ORF) from nucleatide sequences
DOI: 10.5061/dryad.p760b/7
title: GO_Annotation

description: The Gene Ontology annotation of the 'Super' transcriptome assembly based on the RABT method
DOI: 10.5061/dryad.p760b/8
title: Mitochondrial_Site_Coverage

description: The mitochondrial site coverage by the 'Super' transcriptome data
DOI: 10.5061/dryad.p760b/9
title: Transcriptome_comparisons_among_individuals

description: The unique annotated accessions from each individual for comparison
DOI: 10.5061/dryad.rg800/1
title: data_JAB_J00750

description: Spectral measurements of iridescent feathers from male tree swallows captured in 2013-2014 in southern Québec, Canada. A detailed description is available in the last sheet of the excel document.
DOI: 10.5061/dryad.1q2s5/1
title: Free Caudal Vertebral Morphology

description: Linear metrics of free caudal vertebral morphology of eight passeriform taxa.
DOI: 10.5061/dryad.266k4/2
title: plink files for cornell canine dataset

description: chromosome, name, location, alleles for each SNP
DOI: 10.5061/dryad.266k4/3
title: plink files for cornell canine dataset

description: genotypes for each dog at each SNP
DOI: 10.5061/dryad.266k4/4
title: phenotypes

description: phenotypes for each dog
DOI: 10.5061/dryad.2b65b/1
title: dryad

description: Data used in the article. Headings self explanatory
DOI: 10.5061/dryad.31733/16
title: Pb-Podo5-R11T79_R1R2.fastq

description: Podococcus barteri Podo 5 sample - Long range PCR sequencing (MiSeq) - .bam file containing reads after mapping on the chloroplast genome
DOI: 10.5061/dryad.31733/18
title: TOG6208_mt_Run1-TAG-1

description: O. glaberrima TOG6028 sample - Whole genome sequencing (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.
DOI: 10.5061/dryad.31733/19
title: TOG6208_mt_Run1-TAG-6

description: O. glaberrima TOG6028 sample - LR-PCR sequencing (MiSeq) - .bam file containing reads after mapping on the mitochondrial genome. Only reads properly mapped on the chloroplast genome were used.