A quick guide for student-driven community genome annotation

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions

The MYB36 transcription factor orchestrates Casparian strip formation

The endodermis in roots acts as a selectivity filter for nutrient and water transport essential for growth and development. This selectivity is enabled by the formation of lignin-based Casparian strips. Casparian strip formation is initiated by the localization of the Casparian strip domain proteins (CASPs) in the plasma membrane, at the site where the Casparian strip will form. Localized CASPs recruit Peroxidase 64 (PER64), a Respiratory Burst Oxidase Homolog F, and Enhanced Suberin 1 (ESB1), a dirigent-like protein, to assemble the lignin polymerization machinery. However, the factors that control both expression of the genes encoding this biosynthetic machinery and its localization to the Casparian strip formation site remain unknown. Here, we identify the transcription factor, MYB36, essential for Casparian strip formation. MYB36 directly and positively regulates the expression of the Casparian strip genes CASP1, PER64, and ESB1. Casparian strips are absent in plants lacking a functional MYB36 and are replaced by ectopic lignin-like material in the corners of endodermal cells. The barrier function of Casparian strips in these plants is also disrupted. Significantly, ectopic expression of MYB36 in the cortex is sufficient to reprogram these cells to start expressing CASP1–GFP, correctly localize the CASP1–GFP protein to form a Casparian strip domain, and deposit a Casparian strip-like structure in the cell wall at this location. These results demonstrate that MYB36 is controlling expression of the machinery required to locally polymerize lignin in a fine band in the cell wall for the formation of the Casparian strip

Root Suberin Forms an Extracellular Barrier That Affects Water Relations and Mineral Nutrition in Arabidopsis

Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots. Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root and both water movement through the plant and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates and increased water-use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn, and Zn and increases in the accumulation of Na, S, K, As, Se, and Mo in the shoot. Here, we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn, and Zn occurs in the apoplast.</p

Root Suberin Forms an Extracellular Barrier That Affects Water Relations and Mineral Nutrition in Arabidopsis

Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots. Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root and both water movement through the plant and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates and increased water-use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn, and Zn and increases in the accumulation of Na, S, K, As, Se, and Mo in the shoot. Here, we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn, and Zn occurs in the apoplast

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Li F-W, Brouwer P, Carretero-Paulet L, et al. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. NATURE PLANTS. 2018;4(7):460-472

Improved annotation of the insect vector of citrus greening disease: Biocuration by a diverse genomics community

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models.Peer reviewedBiochemistry and Molecular BiologyEntomology and Plant Patholog

Dissecting the molecular mechanism of Casparian strip and endodermal development in Arabidopsis thaliana

The development of the endodermis in the root plays a critical role in the radial transport of water and mineral nutrients into the root stele. Endodermal development begins with the formation of the Casparian strip, a chemically modified region of the cell wall which forms a belt-like structure at the anticlinal wall of the cells in the endodermis. The Casparian strip acts as a barrier to diffusion in the apoplast and provides the endodermal cell polarity that is essential for radial transport. The Casparian strip is primarily composed of lignin. In the region of the root just distal of the root tip the Casparian strip forms the only barrier to diffusion in the apoplast. However, as the endodermis develops in regions of the root distal to the site of primary Casparian strip deposition suberin lamellae are deposited in the apoplast which provides an extra barrier to diffusion. In spite of the critical role of the endodermis in water and solute transport very little is known about the biosynthetic mechanism of Casparian strip formation. Recently, the CASP family of proteins has been shown to be involved in the formation of the Casparian strip by playing an essential role in the formation of the Casparian strip membrane domain. Here, we determine that the Arabidopsis thaliana dirigent-like ESB1 protein localizes to the Casparian strip and expression of the ESB1 gene occurs in that region of the root in which the Casparian strip is developed but that region that lacks suberin lamellae. Importantly, loss of function of ESB1 leads to a malformed Casparian strip. Further, ectopic deposition of suberin in esb1 early in the development of the endodermis is likely to be responsible for the altered leaf ionome of esb1 and also its reduced transpiration. We also observe that in the casp1casp3 double mutant ESB1 is no longer localized to the Casparian strip. The development of the endodermis in the root plays a critical role in the radial transport of water and mineral nutrients into the root stele. Endodermal development begins with the formation of the Casparian strip, a chemically modified region of the cell wall which forms a belt-like structure at the anticlinal wall of the cells in the endodermis. The Casparian strip acts as a barrier to diffusion in the apoplast and provides the endodermal cell polarity that is essential for radial transport. The Casparian strip is primarily composed of lignin. In the region of the root just distal of the root tip the Casparian strip forms the only barrier to diffusion in the apoplast. However, as the endodermis develops in regions of the root distal to the site of primary Casparian strip deposition suberin lamellae are deposited in the apoplast which provides an extra barrier to diffusion. In spite of the critical role of the endodermis in water and solute transport very little is known about the biosynthetic mechanism of Casparian strip formation. Recently, the CASP family of proteins has been shown to be involved in the formation of the Casparian strip by playing an essential role in the formation of the Casparian strip membrane domain. Here, we determine that the Arabidopsis thaliana dirigent-like ESB1 protein localizes to the Casparian strip and expression of the ESB1 gene occurs in that region of the root in which the Casparian strip is developed but that region that lacks suberin lamellae. Importantly, loss of function of ESB1 leads to a malformed Casparian strip. Further, ectopic deposition of suberin in esb1 early in the development of the endodermis is likely to be responsible for the altered leaf ionome of esb1 and also its reduced transpiration. We also observe that in the casp1casp3 double mutant ESB1 is no longer localized to the Casparian strip

Community portal for the Citrusgreening disease resources

<p>Huanglongbing (HLB) is a tritrophic disease complex involving citrus host trees, the Asian citrus psyllid (ACP) insect and a phloem restricted, bacterial pathogen <i>Candidatus </i>Liberibacter asiaticus (CLas). HLB is considered to be the most devastating of all citrus diseases, and there is currently no adequate control strategy. In Florida, an estimated 40-70% of all citrus trees are infected, and HLB effects include production declines (10-20% per year), diminished fruit quality and increased production costs. We have designed a web portal with information for consumers and growers as well as genomics and bioinformatics resources for citrus, ACP and CLas. The JBrowse browser provides the context for expression data and annotated features on the genome. Biocyc Pathway Tools databases model biochemical pathways within each organism and will be used to explore the entire disease complex. Micro-CT analysis of the ACP will be combined with transcriptomics data from different tissues, life stages and sexes to create a 3D atlas that will reveal the internal anatomy of ACP overlaid with the expression profile of different tissues across major life stages. All tools like JBrowse, Blast and the Atlas will connect to a central database containing gene models for citrus, ACP and multiple <i>Candidatus </i>Liberibacter pathogens. The database will allow manual curation so that the community can continuously improve the knowledgebase as more experimental research is published. The database architecture combines custom schemas and the community developed Chado schema (http://gmod.org/wiki/Chado) for compatibility with other genome databases. </p