Focus on the biology of plant genomes

This issue of The Plant Cell includes the first focus issue for the journal, on the Biology of Plant Genomes. Since publication of the first Arabidopsis genome 20 years ago (The Arabidopsis Genome Initiative, 2000), the list of published plant genomes has grown to well over 200, including a handful of ferns, bryophytes, the lycopod Selaginella, nine gymnosperms, about 30 monocots, dozens of eudicots, several magnoliids, and over 50 algal species, and continues to expand apace. In the year 2021, we are now well into the era of leveraging this vast quantity of genome sequence information to gain new understanding of plant evolution, development, and functional biology.

This focus issue includes reviews and research articles highlighting some of the most important recent advances in plant genomics and foreshadowing further key discoveries expected in the near future. Review articles cover 20 years of Arabidopsis genomics (Provart et al., 2021), the diversity of plant NLR proteins and pan-NLRomes (Barragan and Weigel, 2021), and CRISPR screens in plants (Gaillochet et al., 2021). The collection of research articles in this issue reflects the transition from Arabidopsis genomics to genomics of the wider world of diverse plants. Two papers include work on Arabidopsis: Dong et al. (2021) shed light on genome stability during replication in plants, revealing a key molecular role for H3.1K27me1, while Prigozhin and Krasileva (2021) analyze NLR immune receptor complements encoded in 62 ecotypes of Arabidopsis thaliana and 54 lines of Brachypodium distachyon. These authors identify highly variable NLR subfamilies responsible for generation of new receptor specificities. Ten other articles cover a range of topics in diverse species. Forsythe et al. (2021) conducted genome-wide evolutionary rate covariation analyses across 20 diverse angiosperm species to reveal novel plastid–nuclear interactions and suites of coevolving plastid proteostasis genes; Ma et al. (2021a) provide a high-quality assembly, annotation, and analysis of the Pharus latifolius genome, yielding numerous insights into how whole-genome duplication contributed to the origin and diversification of the grass family; Bastiaanse et al. (2021) investigate the effects of gene dosage variation on leaf morphological phenotypes in the Populus genome using a large population of clonally propagated P. nigra × P. deltoides hybrid lines; Wang et al. (2021) present a wheat epigenomic atlas that highlights the interplay between regulatory elements, transcription factors, and epigenetic factors in determining wheat subgenome-divergent spatiotemporal regulation; Diepenbrock et al. (2021) provide a comprehensive genome-level picture of the genetic and molecular control of carotenoids in maize along with a roadmap to accelerate breeding for provitamin A; and in a pair of companion papers in maize, gene expression was analyzed to assess genomic imbalance across the genome in aneuploids of diploid maize (Shi et al., 2021) and in a set of disomic haploids compared to normal haploid maize (Yang et al., 2021). Finally, the issue includes three articles on Chlamydomonas genomics.  Craig et al. (2021) enable a leap forward for comparative genomics with high-quality genome assemblies and annotations for three of the closest relatives of Chlamydomonas reinhardtii: C. incerta, C. schloesseri, and the more distantly related Edaphochlamys debaryana. Ma et al. (2021b) present a new resource and methodology with single-cell RNA-seq analysis in Chlamydomonas cultures, revealing that the heterogeneity in bulk cultures is largely driven by diurnal cycle phases. And Salomé and Merchant (2021) dive into a large dataset to present a coexpression network of Chlamydomonas genes to derive deep insights into coexpressed genes and to help foster gene function discovery. These three papers represent a fantastic resource and will greatly expand our understanding of Chlorophycean and other photosynthetic algal biology.

Additional articles in this focus area published roughly 1 year before or after this issue will be included in a focus collection on the journal website. Two focus issues are in the works for 2022: a focus on Cell Biology (submissions deadline in May 2021; publication January 2022) and Plant–Microbe Interactions (deadline for submissions in September 2021; publication in May 2022). Please visit https://aspb.org/publications/tpcfocus for more information and consider submitting your best work in these areas. We will continue to plan for two focus issues per year, to attract and publish some of the highest quality research on topics of high currency and interest in the community.