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      Evolution and expression of LEAFY genes in ferns and lycophytes

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          Abstract

          Background

          The LEAFY ( LFY) transcription factors are present in algae and across land plants. The available expression and functional data of these genes in embryophytes suggest that LFY genes control a plethora of processes including the first zygotic cell division in bryophytes, shoot cell divisions of the gametophyte and sporophyte in ferns, cone differentiation in gymnosperms and floral meristem identity in flowering plants. However, their putative plesiomorphic role in plant reproductive transition in vascular plants remains untested.

          Results

          We perform Maximum Likelihood (ML) phylogenetic analyses for the LFY gene lineage in embryophytes with expanded sampling in lycophytes and ferns. We recover the previously identified seed plant duplication that results in LEAFY and NEEDLY paralogs. In addition, we recover multiple species-specific duplications in ferns and lycophytes and large-scale duplications possibly correlated with the occurrence of whole genome duplication (WGD) events in Equisetales and Salviniales. To test putative roles in diverse ferns and lycophytes we perform LFY expression analyses in Adiantum raddianum, Equisetum giganteum and Selaginella moellendorffii. Our results show that LFY genes are active in vegetative and reproductive tissues, with higher expression in early fertile developmental stages and during sporangia differentiation.

          Conclusions

          Our data point to previously unrecognized roles of LFY genes in sporangia differentiation in lycophytes and ferns and suggests that functions linked to reproductive structure development are not exclusive to seed plant LFY homologs.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s13227-021-00188-9.

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          Most cited references66

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          Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

          Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here, we present the Trinity methodology for de novo full-length transcriptome reconstruction, and evaluate it on samples from fission yeast, mouse, and whitefly – an insect whose genome has not yet been sequenced. Trinity fully reconstructs a large fraction of the transcripts present in the data, also reporting alternative splice isoforms and transcripts from recently duplicated genes. In all cases, Trinity performs better than other available de novo transcriptome assembly programs, and its sensitivity is comparable to methods relying on genome alignments. Our approach provides a unified and general solution for transcriptome reconstruction in any sample, especially in the complete absence of a reference genome.
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            MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

            K Katoh (2002)
            A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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              CDD/SPARCLE: the conserved domain database in 2020

              As NLM’s Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
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                Author and article information

                Contributors
                lucia.pabon@udea.edu.co
                Journal
                EvoDevo
                Evodevo
                EvoDevo
                BioMed Central (London )
                2041-9139
                8 January 2022
                8 January 2022
                2022
                : 13
                : 2
                Affiliations
                [1 ]GRID grid.412881.6, ISNI 0000 0000 8882 5269, Facultad de Ciencias Exactas y Naturales, Instituto de Biología, , Universidad de Antioquia, ; Medellín, Colombia
                [2 ]GRID grid.288223.1, ISNI 0000 0004 1936 762X, The New York Botanical Garden, ; Bronx, NY USA
                [3 ]GRID grid.423145.5, ISNI 0000 0001 2158 9350, Botanical Research Institute of Texas, ; Fort Worth, TX USA
                [4 ]GRID grid.412881.6, ISNI 0000 0000 8882 5269, Centro Nacional de Secuenciación Genómica, Facultad de Medicina, , Sede de Investigación Universitaria, Universidad de Antioquia, ; Medellín, Colombia
                Author information
                http://orcid.org/0000-0003-3528-8078
                Article
                188
                10.1186/s13227-021-00188-9
                8742948
                34998428
                e512aebc-3949-43ed-a1db-c58ca50d3c2a
                © The Author(s) 2022

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 23 September 2021
                : 18 December 2021
                Funding
                Funded by: Fundación para la Promoción de la Investigación y la Tecnología
                Award ID: Project Number 4413
                Award Recipient :
                Funded by: Universidad de Antioquia
                Award ID: Convocatoria de Sostenibilidad 2018-2019
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2022

                Developmental biology
                leafy,ferns,lycophytes,reproductive transition,sporogenesis
                Developmental biology
                leafy, ferns, lycophytes, reproductive transition, sporogenesis

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