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Hyalella azteca Official Gene Set v1.0

    The Hyalella azteca genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Hyalella azteca research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The OGS is an integration of automatic gene predictions from Maker with manual annotations by the research community (via the Apollo manual annotation software).

    Cacao Genome Database

      The release of the cacao genome sequence will provide researchers with access to the latest genomic tools, enabling more efficient research and accelerating the breeding process, thereby expediting the release of superior cacao cultivars. The sequenced genotype, Matina 1-6, is representative of the genetic background most commonly found in the cacao producing countries, enabling results to be applied immediately and broadly to current commercial cultivars.  Matina 1-6 is highly homozygous which greatly reduces the complexity of the sequence assembly process. While the sequence provided is a preliminary release, it already covers 92% of the genome, with approximately 35,000 genes. We will continue to refine the assembly and annotation, working toward a complete finished sequence.

      ARS Microbial Genomic Sequence Database Server

        This database server is supported in fulfilment of the research mission of the Mycotoxin Prevention and Applied Microbiology Research Unit at the National Center for Agricultural Utilization Research in Peoria, Illinois. The linked website provides access to gene sequence databases for various groups of microorganisms, such as Streptomyces species or Aspergillus species and their relatives, that are the product of ARS research programs. The sequence databases are organized in the BIGSdb (Bacterial Isolate Genomic Sequence Database) software package developed by Keith Jolley and Martin Maiden at Oxford University.

        Gramene

          Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.

          Ricebase

            Ricebase ([https://ricebase.org](https://ricebase.org)) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data.

            Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola: A small fungal genome with an increased cohort of genes associated with loss of virulence

              Boxwood plants are affected by many different diseases caused by fungi. Some boxwood diseases are deadly and quickly kill the infected plants, but with others, the plant can survive and even thrive when infected. The fungus that causes volutella blight is the most common of these weak boxwood pathogens. Even the healthiest boxwood plants are infected by the volutella fungus, and often there are no signs that the plants are hurt by the infection. In order to understand why the volutella blight fungus is such a weak pathogen and to understand the genetic mechanisms it uses to interact with boxwood, the complete genome of the volutella fungus was sequenced and characterized. These datasets are generated from the genome sequence of *Pseudonectria foliicola*, strain ATCC13545, the fungus responsible for volutella disease of boxwood. Datasets include the nuclear genome and mitochondrial genome assemblies (sequenced using Illumina technology), the predicted gene model dataset generated using MAKER, the multiple sequence alignment of single-copy orthologs used for phylogenetic analysis, CMAP files generated from SimpleSynteny analysis of mitogenomes, and high quality photographic images.

              Leptinotarsa decemlineata genome annotations v0.5.3

                This dataset presents the Leptinotarsa decemlineata gene set BCM_v_0.5.3, which was generated computationally. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Leptinotarsa decemlineata genome assembly 1.0.

                PeanutBase

                  PeanutBase ([peanutbase.org](https://peanutbase.org)) is the primary genetics and genomics database for cultivated peanut and its wild relatives. It houses information about genome sequences, genes and predicted functions, genetic maps, markers, links to germplasm resources, and maps of peanut germplasm origins.

                  Diaphorina citri Official Gene Set v1.0

                    This gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. 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.

                    Data from: Genomic analyses of dominant US clonal lineages of Phytophthora infestans reveals a shared ancestry for US11 and US18 and a lack of recently shared ancestry for all other US lineages

                      The populations of the potato and tomato late blight pathogen, Phytophthora infestans, in the US are well known for emerging repeatedly as novel clonal lineages. These successions of dominant clones have historically been named US1 through US24, in order of appearance, since their first characterization using molecular markers. Hypothetically, these lineages can emerge by descent from prior lineages or as novel, independent lineages.