BioContainers: An open-source and community-driven framework for software standardization

Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/.publishedVersio

Tracing ancestor rice of Suriname Maroons back to its African origin

African rice (Oryza glaberrima) and African cultivation practices are said to have influenced emerging colonial plantation economies in the Americas(1,2). However, the level of impact of African rice practices is difficult to establish because of limited written or botanical records(2,3). Recent findings of O. glaberrima in rice fields of Suriname Maroons bear evidence of the high level of knowledge about rice among African slaves and their descendants, who consecrate it in ancestor rituals(4,5). Here we establish the strong similarity, and hence likely origin, of the first extant New World landrace of O. glaberrima to landraces from the Upper Guinean forests in West Africa. We collected African rice from a Maroon market in Paramaribo, Suriname, propagated it, sequenced its genome(6) and compared it with genomes of 109 accessions representing O. glaberrima diversity across West Africa. By analysing 1,649,769 single nucleotide polymorphisms (SNPs) in clustering analyses, the Suriname sample appears sister to an Ivory Coast landrace, and shows no evidence of introgression from Asian rice. Whereas the Dutch took most slaves from Ghana, Benin and Central Africa(7), the diaries of slave ship captains record the purchase of food for provisions when sailing along the West African Coast(8), offering one possible explanation for the patterns of genetic similarity. This study demonstrates the utility of genomics in understanding the largely unwritten histories of crop cultures of diaspora communities.Biosystematics group of Wageningen University; Naturalis Biodiversity Center (Leiden); NSF Plant Genome [IOS-1202803, IOS-1126971]; TKI-Horticulture Grant; US National Science Foundation; NYU Abu Dhabi Research Institute; AXA Chair in Genome Biology and Evolutionary Genomics6 month embargo. First available online 03 October 2016.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Osmopriming-associated genes in Poincianella pyramidalis

Osmopriming of seeds can increase seed vigour, allowing faster germination and field emergence, especially under adverse field conditions. The restricted imbibition during priming treatments reactivates metabolism although germination will be prevented. In order to identify and characterize genes that are involved in the improvement of vigour of Poincianella pyramidalis (Catingueira) seeds upon priming, we produced two different Suppression Subtractive Hybridization (SSH) cDNA libraries. These were a Forward and Reverse subtraction of cDNA samples isolated from untreated dry seeds (unprimed) and osmoprimed seeds. The two different libraries were sequenced by Illumina GAII next generation sequencing, resulting in almost 20 million reads that could be assigned to 5298 different contigs. Of these, 999 were only found in the unprimed seeds library and 2711 were specific for osmoprimed seeds. The contigs were annotated and subjected to gene set enrichment analysis and differential expression of several genes was confirmed by qRT-PCR analysis. The identified differentially expressed genes might play an important role in vigour improvement upon priming and may be potential markers for tolerance to water stress in P. pyramidalis seeds.</p

BioContainers: An open-source and community-driven framework for software standardization

Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/

The genome of the stress-tolerant wild tomato species Solanum pennellii

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.Fil: Bolger, Anthony. Aachen University; Alemania. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Scossa, Federico. Institut Max Planck fur Molekulare Physiologie; Alemania. Consiglio per la Ricerca in Agricoltura e l'Analisi del l'Economía Agraria; ItaliaFil: Bolger, Marie E.. Institut Max Planck fur Molekulare Physiologie; Alemania. Forschungszentrum Jülich; AlemaniaFil: Lanz, Christa. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Maumus, Florian. Institut National de la Recherche Agronomique; FranciaFil: Tohge, Takayuki. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Quesneville, Hadi. Institut National de la Recherche Agronomique; FranciaFil: Alseekh, Saleh. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Sørensen, Iben. Cornell University; Estados UnidosFil: Lichtenstein, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Fich, Eric A.. Cornell University; Estados UnidosFil: Conte, Mariana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas; ArgentinaFil: Keller, Heike. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Schneeberger, Korbinian. Institut Max Planck fur Molekulare Physiologie; Alemania. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Schwacke, Rainer. Institut Max Planck fur Molekulare Physiologie; Alemania. Forschungszentrum Jülich; AlemaniaFil: Ofner, Itai. The Hebrew University of Jerusalem; IsraelFil: Vrebalov, Julia. Cornell University; Estados UnidosFil: Xu, Yimin. Cornell University; Estados UnidosFil: Osorio, Sonia. Institut Max Planck fur Molekulare Physiologie; Alemania. Universidad de Málaga; EspañaFil: Aflitos, Saulo Alves. University of Agriculture Wageningen; Países BajosFil: Schijlen, Elio. University of Agriculture Wageningen; Países BajosFil: Jiménez Goméz, José M.. Max Planck Institute for Plant Breeding Research; Alemania. Institut National de la Recherche Agronomique; FranciaFil: Ryngajllo, Malgorzata. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Kimura, Seisuke. University of California at Davis; Estados UnidosFil: Kumar, Ravi. University of California at Davis; Estados UnidosFil: Koenig, Daniel. Institut Max Planck fur Molekulare Physiologie; Alemania. University of California at Davis; Estados UnidosFil: Headland, Lauren R.. University of California at Davis; Estados UnidosFil: Maloof, Julin N.. University of California at Davis; Estados UnidosFil: Sinha, Neelima. University of California at Davis; Estados UnidosFil: Van Ham, Roeland C. H. J.. University of Agriculture Wageningen; Países Bajo

The genome of the stress-tolerant wild tomato species Solanum pennellii.

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm