Characterization of chitin deacetylase genes in the Diaphorina citri genome

Chitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of higher order chitin structures, such as long fibers and bundles, that contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also play a role in bacterial defense. Here we report the characterization of four CDA genes from the Asian citrus psyllid, Diaphorina citri, laying the groundwork for future study of these genes. D. citri is the vector for Candidatus Liberibacter asiaticus (CLas), which is responsible for the global outbreak of Huanglongbing (citrus greening) disease. The manual annotation was done as part of a collaborative community annotation project (https://citrusgreening.org/annotation/index).

Mapping Quantitative Trait Loci for Cold Tolerance in Rice under Germination Stage by Whole Genome Resequencing and Analysis of Candidate Genes

Low-temperature stress significantly affects rice growth and causes serious loss of yield in temperate and high-altitude areas of the world. Rice lacks cold tolerance (CT) at germination stage, which reduces seedling vigor, hinders crop establishment and crop growth, and even affect direct-seeded rice. A chromosome segment substitution line (CSSL) population, including 271 lines, was derived from cold-tolerant donor wild rice Y11 (Oryza rufipogon Griff.) crossed with cold-sensitive rice variety GH998 to explore new genetic resource with CT and further investigate quantitative trait loci (QTLs) responsible for germination properties under low temperature. The germination rates of Y11 and GH998 were 95% and 73.33%, respectively, under cold stress. The range of variance of the germination rate in the CSSLs was between 0% and 98.33%. In addition, the CSSLs and parents were sequenced via whole genome resequencing. Results showed 33.46, 33.36, and 475.65 Gbp of clean data of GH998, Y11, and CSSLs, respectively. In 12 linkage groups, the general map distance was 941.49 cM, while the average map distance was 0.63 cM. On thebasis of 1484 bins, a high-density linkage map of the CSSLs was developed. The average distance of the linkage map ranged from 0.42 cM to 1.39 cM. The phenotype of CSSLs under low temperature and 615,466 single nucleotide polymorphisms (SNPs) between Y11 and GH998 were used for QTL analysis. Two QTLs, namely, low-temperature germination 8 (qLTG8) and qLTG11, were responsible for the germination ability under low temperature in rice. qLTG8 was mapped on chromosome 8, and it explained 14.55% of the total phenotypic variation explained (PVE) during the germination stage. qLTG8 was in 195.5 kb, and 32 genes were predicted based on the Rice Genome Annotation Project. qLTG11 was located on chromosome 11, and it explained 14.31% of the total PVE during the germination stage. qLTG11 was mapped at a narrow distance in 78.83 kb, and only 12 genes fall within this range according to the Rice Genome Annotation Project. The expression patterns of these 32 genes in the qLTG8 region demonstrated that LOC_Os08g01120, LOC_Os08g01140, LOC_Os08g01390, LOC_Os08g01170, and LOC_Os08g01380 were highly induced by cold stress in Y11 compared with GH998. The expression patterns of 12 genes in the qLTG11 region suggested that LOC_Os11g32880 and LOC_Os11g32940 were highly induced by cold stress in Y11 compared with GH998. This study provides an effective method, i.e., constructing CSSLs of wild rice, to explore excellent genes of wild rice and create new genetic resources. The results also provide a basis for identifying the genes underlying qLTG8 and qLTG11, indicating that QTL could be used for genetic improvement of CT in cultivar rice.

Lexicons, Literacies and Design Futures

As the world in which we live becomes more complex and contested, economically and politically but also in terms of rapid and long-lasting environmental change, design education faces new demands and challenges. We frame and situate these in terms of what we call “design futures literacies.” At stake in such a framing is a rethinking of design’s priorities in the context of climate change and resource use and reuse in futures that are uncertain, contingent and emergent. The article positions design as having shifted away from a techno-modernist design solutionism and to how it may engage in shaping futures through experimentation and exploration in the critical and productive engagement with techno-cultural life. These arguments are located within the prior experience of the transdisciplinary team of co-authors as well as a European level project between four leading design universities. The article takes up their first work package on the co-creation of a Lexicon for Design Futures Literacies and early experimentation towards generating resources and experience for its wider use. The article addresses the largely under articulated relations between language and design (from lexis to discourse). First, we present the development of an alphabetic, lexical semantic set and core grouping of design and futures terms. This vocabulary, drawn from a range of sources and experiences, is linked to the design of a related lexically centred card game. Second, the focus on vocabulary was extended to a section on situating lexis in cultural historical contexts, 3-dimensional haptic form giving and the language of abstraction. This was achieved via reference to a design narrative fiction experiment on emerging technologies and a historical costume annotation project as a prompt for making connections between items from the lexicon and modelling abstract forms in clay. Third, in collaboration with a government ministry and a design council, students developed four future digital urban living scenarios with trust as their central focus. “Languaging” the future was embodied in physical scenarios open to the public, connected to a professional seminar and to international research events where verbal descriptions, explanations and reflections were voiced by the students alongside their educator-researcher. The article closes with suggestions that there is further opportunity for attention to lexis and multimodal discourse modes in shaping design futures literacies, within and across the project but also in practice, in policy and for and as design pedagogy.

Ten steps to get started in Genome Assembly and Annotation

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).

In silico analysis of transcription factor binding sites in promoters of germin-like protein genes in rice

Germins (GERs) and germin-like proteins (GLPs) play important roles in responses to various stresses; however, their function is still not fully understood. Significant insight into their function can be obtained by analyzing their promoters. In the present study, the 5' upstream promoters (1000 bp) of 43 Asian rice (Oryza sativa var. Japonica) GLP genes were retrieved from the Plant Ensemble, based on the Rice Annotation Project database (RAP-DB). Phylogenetic analysis via MEGA6 showed a narrow genetic background (0.2%) with a Tajima neutrality value (?) of 0.69. Overall, 4234 transcription factor (TF) binding sites (TFBSs) were found on chromosomes 1, 2, 3, 4, 5, 8, 9, 11 and 12 via ?MatInspector? from 90 different TF families using a total of 444 families. Common TFs and DiAlign analyses showed that arabidopsis homeobox protein (AHBP), MYB-like proteins (MYBL) and vertebrate TATA-box-binding protein (VTBP) were the most abundant, common and evolutionarily conserved elements in the upstream region from 0 to -800. Finding their mutual interaction via Farmworker analysis uncovered three new cisregulatory modules (VTBP_VTBP, MYBS_MYBS, and AHBP_VTBP), which appear to be decisive for OsGLP regulation. In silico functional analysis via ModelInspector revealed 77 cis-regulatory modules, each comprised of two elements, among which DOFF_OPAQ_03 and GTBX_MYCL_01 were the most frequent and mostly found on chromosome 8 and 12, indicating that the combinatorial interaction of these elements has a fundamental role in various biological processes. The study revealed the importance of these elements in regulating OsGLP expression that will help in predicting the role of these genes in various stresses, and can have application in biotechnology.

An XML engine to model and query multimodal concurrent linguistic annotations

This paper presents an XML engine defined to model and query multimodal concurrent annotated data. This work stands in the context of the OTIM (Tools for Multimodal Annotation) project which aims at developing conventions and tools for multimodal annotation of a large conversational French speech corpus; it groups together Social Science and Computer Science researchers. Within OTIM, our objective is to provide linguists with a unique framework to encode and manipulate numerous linguistic domains: morpho-syntax, prosody, phonetics, disfluencies, discourse, gesture and posture. For that, it has to be possible to bring together and align all the different pieces of information (called annotations) associated to a corpus. We propose a complete pipeline from the annotation step to the management of the data within an XML Information System. This pipeline first relies on the formalisation of the linguistic knowledge and data within a OTIM specific XML format. A Java framework is proposed for interfacing with both linguists specific annotation tools and XML Information System. Finally, the querying of multimodal annotations within the XML information system using XQuery is presented. As annotations are time aligned, an extension of XQuery to Allen temporal relations is proposed. The paper conclude on a discussion about the interest of a pure XML approach for linguistic annotations information system and the question of the integration of the semantic within the pipeline.