WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States

Premise of the study: Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. Methods and Results: A set of command line–based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. Conclusions: WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA

The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding

Bioinformatic Workflows for Generating Complete Plastid Genome Sequences - An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content

Pemasaran Hijau Yang Semakin Menjadi Kebutuhan Dalam Dunia Bisnis

Green marketing is a type of marketing where a company sells a product that is envi-ronmentally friendly. In the concept of green marketing, a company has done greenmarketing since the beginning of the production process which transform raw materi-als into environmentally friendly finished product, called green product. The growingglobal warming make the green marketing is a major issue in today\u27s business world.Green marketing has become a necessity for both producers and consumers for thecreation of a healthy environment. A company can do green marketing that matchesto the company\u27s business. Implementation of green marketing can cover many ac-tivities depending on what the company wants to do. Automotive manufacturers arean example of a company that must implement a comprehensive green marketingbecause its products could potentially damage the environment due to pollution fromvehicle fumes

Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly–A Case Study in the Narrow Endemic Calligonum bakuense

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice

Pengaruh Macam Bahan Organik Dan Inokulum Rhizobium Terhadap Pertumbuhan Dan Hasil Tanaman Kedelai (Glycine Max (L.) Merril)

Kedelai (Glycine max (L.) Merril) merupakan tanaman pangan yang penting di Indonesia. Sebagai tanaman golongan Leguminoceae, tanaman kedelai mampu mengadakan simbiosis dengan bakteri tertentu sehingga dapat langsung memfiksasi nitrogen dari udara. Tujuan penelitian ini ialah mempelajari pengaruh interaksi macam bahan organik dan dosis legin terhadap peningkatan pertumbuhan dan hasil tanaman kedelai (Glycine max (L.) Merril). Hipotesis yang diajukan ialah macam bahan organik dapat mempengaruhi kebutuhan dosis legin untuk meningkatkan pertumbuhan dan hasil tanaman kedelai (Glycine max (L.) Merril). Penelitian dilaksanakan di Kebun Percobaan Fakultas Pertanian desa Jatikerto, kecamatan Kromengan, kabupaten Malang. Penelitian dilaksanakan pada bulan Juni 2014 sampai bulan September 2014. Alat yang digunakan pada penelitian ialah Leaf Area Meter (LAM), timbangan analitik, meteran dan oven. Bahan yang digunakan adalah benih kedelai varietas Grobogan. Perlakuan yang diberikan yaitu faktor satu adalah pemberian bahan organik yang terdiri dari: B1=tanpa aplikasi bahan organik, B2=residu biochar dan B3= kompos 10 ton ha-1. Faktor kedua adalah penggunaan legin yang terdiri dari: L1 = tanpa legin, L2 = dosis legin 8 g kg-1 dan L3 = dosis legin 12 g kg-1. Hasil penelitian menunjukkan penambahan bahan organik kompos 10 ton ha-1 dan residu biochar tidak mempengaruhi kebutuhan dosis legin. Kompos 10 ton ha-1 nyata untuk meningkatkan jumlah polong per tanaman kedelai (Glycine max (L.) Merril) sebesar 71,21 %. Dosis legin tidak nyata terhadap hasil panen tanaman kedelai (Glycine max (L.) Merril)

Phylogenetic relationships and arbuscular mycorrhizal diversity of Tolpis Adans. (Asteraceae), with special reference to island endemism and biogeography

textThe plant genus Tolpis (Asteraceae) is a predominantly insular plant lineage. It inhabits four of the five archipelagoes that comprise the Atlantic region of Macaronesia and also occurs in Mediterranean Europe and North Africa. Twelve species are currently recognized in Tolpis, of which ten are insular and two continental. The majority of the insular species inhabit the five western Canarian islands, where they constitute endemics to specific ecological habitats. A comprehensive molecular phylogeny of Tolpis is generated via DNA sequences of one nuclear ribosomal and two low-copy nuclear DNA markers. Considerable phylogenetic uncertainty among inferred tree topologies is detected, and incongruence between these topologies is resolved via statistical hypotheses testing. The extant diversity of the genus is identified to be the result of two independent colonization pathways and adaptive radiations on several islands. Moreover, potential hybridization is detected between species that inhabit different islands and archipelagoes, indicating a more widespread historical distribution of the genus. Details of the biogeographic history of Tolpis are inferred via ancestral area reconstructions under parsimony and likelihood optimality criteria. The hypothesis that Tolpis may have undergone a back-dispersal from an island to a continental habitat is also tested. Uncertainty in taxon cladograms owing to the presence of hybrid or allopolyploid taxa is characterized and a potential adjustment strategy evaluated. Averaging reconstruction results over all optimal phylogenetic trees and the manual pruning of cloned DNA sequences are found potential adjustment strategies against the impact of topological uncertainty owning to hybrid or allopolyploid taxa. Adjusted ancestral area reconstructions in Tolpis do not support the scenario that the genus has undergone a reverse colonization of the continent. In addition to the phylogenetic and biogeographic history of the genus, the diversity of symbiotic mycorrhizal fungi associated with Tolpis is characterized. A molecular survey using two nuclear ribosomal DNA markers and 454 pyrosequencing is performed. Particular emphasis is placed on the quality filtering of resulting fungal DNA sequences, the generation of operational taxonomic units, and their taxonomic assignment via similarity searches against DNA sequence databases. Numerous potentially novel fungal genotypes are identified.Plant Biolog

Proceedings of the AMURGA International Conferences on Island Biodiversity, 2011

Summary. Introduction (p. 8) -- Preface (p. 10) -- 1. Island Biogeography -- The importance of windows of opportunity for long-distance dispersal to or from oceanic islands: examples from the Macaronesian archipelago / by José María Fernández Palacios et al. (p. 16) -- Integrative phylogenetic evidence on the origin of island endemics in the Mediterranean region: Comparisons between oceanic and continental fragment islands / by Elena Conti (p. 24) -- Bayesian biogeography finds its roots: Statistical models in island biogeography / by Isabel Sanmartín (p. 38) -- A comparison of bryophyte diversity in the Macaronesian Islands. Island versus habitat approach / by Juana María González-Mancebo et al. (p. 52) -- Macaronesia: a refugium and obligate custom office for Atlantic bryophyte species in transit from and towards Europe / by Alain Vanderpoorten et al. (p. 68) -- 2. Genetic Diversity and Ecology in the Canaries -- Sexual systems in canarian flora. Evolutionary pathways to gender dimorphism and dioecy / by Julia Pérez de Paz et al. (p. 78) -- Islands within islands: historical and ecological constraints explain disjunct distribution between Navaea phoenicea populations / by Javier Fuertes Aguilar et al. (p. 92) -- Genetic diversity of Canarian endemisms revealed by microsatellites: knowledge after one decade of analysis / by Pedro A. Sosa et al. (p. 94) -- A “Tree of Life” for the Canarian endemic trees: a first step toward the Phylogenetic Diversity of the archipelago’s flora / by Ruth Jaén-Molina et al. (p. 104) -- 3. Evolutionary Processes -- Contribution of natural hybridization to plant evolution in oceanic islands (and elsewhere). Is a conceptual synthesis possible? / by Gonzalo Nieto Feliner (p. 124) -- Long-distance dispersal by wind / by Jesús Muñoz (p. 134) -- The surfing syngameon hypothesis: implications for the genetic and taxonomic diversities of the present Canarian flora / by Juli Caujapé-Castells (p. 136) -- Preliminary investigations of correlated diversification between plants and their associated arbuscular mycorrhizal fungi in Macaronesia / by Bob Jansen et al. (p. 146) -- Does the Linnean shortfall explain the Azores diversity enigma? / by Mark A. Carine (p. 156) -- 4. Plant Life Out of Macaronesia – The Reproductive Biology of Island Plants: the Juan Fernandez and Canary Islands / by Dan Crawford et al. (p. 166) -- Genetic diversity and phylogeography in Western Mediterranean islands: what we do know and what we should know / by Josep A. Rossello et al. (p. 178) -- What can tell us genome organization about plant evolution in Mediterranean continental islands? / by Marcela Rosato et al. (p. 180) -- Contrasting patterns of plant evolution in the Canarian and Galapagos islands: the origin of dispersal and colonization / by Pablo Vargas et al. (p. 182) -- Floristic relationships between Macaronesia, mainly Canary Islands, and East Africa / by Arnoldo Santos-Guerra (p. 192) -- 5. Macaronesian Floras -- Taxonomy of island plants: a proposal for a Flora of Macaronesia / by David Bramwell (p. 204) -- SW Morocco: An obvious step for understanding the Canary Islands Flora / by Jorge Alfredo Reyes-Betancort & Arnoldo Santos-Guerra (p. 206) -- Conservation strategies for the Azorean priority taxa: what are the molecules telling us? / by Mónica Moura (p. 218) -- A phylogeny for the Macaronesian flora and how we can use it to predict potential invaders and identify hotspots of genetic diversity / by Hanno Schaefer (p. 220) -- Present and emerging knowledge on the evolution, diversity and conservation of the canarian flora. / by Maria Romeiras & Maria Cristina Duarte (p. 238)Biological Sciences, School o

airpg: automatically accessing the inverted repeats of archived plastid genomes

Abstract Background In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations. Results We introduce airpg, a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using airpg, followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations. Conclusion The number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. airpg enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index at http://pypi.python.org/pypi/airpg

Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships

The plastid genomes of early-diverging angiosperms were among the first land plant plastomes investigated. Despite their importance to understanding angiosperm evolution, no investigation has so far compared gene content or gene synteny of these plastid genomes with a focus on the Nymphaeales. Here, we report an evaluation and comparison of gene content, gene synteny and inverted repeat length for a set of 15 plastid genomes of early-diverging angiosperms. Seven plastid genomes of the Nymphaeales were newly sequenced for this investigation. We compare gene order and inverted repeat (IR) length across all genomes, review the gene annotations of previously published genomes, generate a multi-gene alignment of 77 plastid-encoded genes and reconstruct the phylogenetic relationships of the taxa under study. Our results show that gene content and synteny are highly conserved across early-diverging angiosperms: All species analyzed display complete gene synteny when accounting for expansions and contractions of the IRs. This conservation was initially obscured by ambiguous and potentially incorrect gene annotations in previously published genomes. We also report the presence of intact open reading frames across all taxa analyzed. The multi-gene phylogeny displays maximum support for the families Cabombaceae and Hydatellaceae, but no support for a clade of all Nymphaeaceae. It further indicates that the genus Victoria is embedded within Nymphaea. Plastid genomes of Trithuria were found to deviate by numerous substitutions and length changes in the IRs. Phylogenetic analyses further indicate that a previously published plastome named Nymphaea mexicana falls into a clade of N. odorata and should be re-evaluated