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Data from: Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

    For genome assembly of *C. zofingiensis* strain SAG 211–14, we used a hybrid approach blending short reads (Illumina), long reads (Pacific Biosciences of California), and whole-genome optical mapping (OpGen) (SI Appendix, SI Text and Datasets S1–S19, and refer to SI Appendix, Datasets Key). The combined power of these approaches yielded a high-quality haploid nuclear genome of *C. zofingiensis* of ∼58 Mbp distributed over 19 chromosomes (Fig. 2) in the tradition of model organism projects, as opposed to the fragmentary “gene-space” assemblies typical of modern projects using high-throughput methods and associated software. Approximately 99% of reads from the Illumina genomic libraries were accounted for, and nonplaceholder chromosomal sequence covers ∼94% of the optical map. Because no automated pipeline was found able to achieve the desired quality, methods are described in SI Appendix, SI Text.

    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.