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      Non‐seed plants are emerging gene sources for agriculture and insect control proteins

      1 , 2
      The Plant Journal
      Wiley

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          SUMMARY

          The non‐seed plants (e.g., charophyte algae, bryophytes, and ferns) have multiple human uses, but their contributions to agriculture and research have lagged behind seed plants. While sharing broadly conserved biology with seed plants and the major crops, non‐seed plants sometimes possess alternative molecular and physiological adaptations. These adaptations may guide crop improvements. One such area is the presence of multiple classes of insecticidal proteins found in non‐seed plant genomes which are either absent or widely diverged in seed plants. There are documented uses of non‐seed plants, and ferns for example have been used in human diets. Among the occasional identifiable toxins or antinutritive components present in non‐seed plants, none include these insecticidal proteins. Apart from these discrete risk factors which can be addressed in the safety assessment, there should be no general safety concern about sourcing genes from non‐seed plant species.

          Significance Statement

          Lower plants such as ferns and mosses are underexplored resources for agriculture. Recent investigations have revealed that lower plants contain genes for insecticidal proteins that are now being leveraged for transgenic crop improvement.

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          Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

          Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.
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            One thousand plant transcriptomes and the phylogenomics of green plants

            Green plants (Viridiplantae) include around 450,000–500,000 species 1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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              The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.

              We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
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                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                The Plant Journal
                The Plant Journal
                Wiley
                0960-7412
                1365-313X
                October 2023
                July 31 2023
                October 2023
                : 116
                : 1
                : 23-37
                Affiliations
                [1 ] Corteva Agriscience, Trait Discovery Johnston Iowa 50131 USA
                [2 ] Corteva Agriscience, Regulatory and Stewardship Johnston Iowa 50131 USA
                Article
                10.1111/tpj.16349
                93a0b1e9-acce-4f9a-8f71-5a752aace311
                © 2023

                http://creativecommons.org/licenses/by-nc-nd/4.0/

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