Long-read transcriptome and other genomic resources for the angiosperm <i>Silene noctiflora</i>

Williams, Alissa M.; Itgen, Michael W.; Broz, Amanda K.; Carter, Olivia G.; Sloan, Daniel B

doi:10.1093/g3journal/jkab189

Cited by 10 publications

(20 citation statements)

References 88 publications

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“…The species described in this work include among others also some of the commonest in Europe and the Mediterranean region, and also some of the best characterized genetically. Whole-genome draft sequence data are so far available from the widespread dioecious species Silene latifolia [ 31 , 32 , 33 ] and from its relatively close widespread hermaphrodite relative— S. noctiflora [ 34 ]. The genus Silene serves as an important model system in ecology and evolution [ 35 ].…”

Section: Discussionmentioning

confidence: 99%

New Geometric Models for Shape Quantification of the Dorsal View in Seeds of Silene Species

Rodríguez-Lorenzo

Gómez

Juan

et al. 2022

Plants

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The description of shape in Silene seeds is based on adjectives coined by naturalists in the 19th century. The expressions reniform, dorso plana, and dorso canaliculata were applied in reference to lateral or dorsal views of seeds, but the characters described can be submitted now to an analytical description by quantitative methods, allowing shape quantification and the comparison between species or populations. A quantitative morphological analysis is based on the comparison with geometric models that adjust to the shape of seeds. Morphological analysis of the dorsal view of Silene seeds based on geometric models is applied here to 26 seed populations belonging to 12 species. According to their dorsal views, the seeds are classified as convex and non-convex. New geometric models are presented for both types, including figures such as super-ellipses and modified ellipses. The values of J index (percent of similarity of a seed image with the model) are obtained in representative seed samples from diverse populations and species. The quantitative description of seed shape based on the comparison with geometric models allows the study of variation in shape between species and in populations, as well as the identification of seeds in Silene species. The method is of application to other plant species.

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Section: Discussionmentioning

confidence: 99%

New Geometric Models for Shape Quantification of the Dorsal View in Seeds of Silene Species

Rodríguez-Lorenzo

Gómez

Juan

et al. 2022

Plants

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“…Full-length mRNA sequences are useful when inferring which specific gene copies have N-terminal extensions because plants often have multicopy genes with high sequence similarity. Previously generated genome assemblies from the same species (Krasovec et al, 2018; Warren et al, 2021; Williams et al, 2021) were also searched for genes and putative transit peptides potentially missed by Iso-Seq analysis due to lower expression levels.…”

Section: Resultsmentioning

confidence: 99%

“…Tissue generation, RNA extraction, and Iso-Seq library construction for S. noctiflora were done in a previously described study (Williams et al, 2021), while data for the other four Sileneae species were newly generated for this study. The following seed collections or accessions were used: A. githago Kew Gardens Millennium Seed Bank (0053084), S. vulgaris S9L (Sloan et al, 2012a), S. latifolia UK2600 (from the line originally used for mitogenome sequencing in (Sloan et al, 2010)), and S. conica ABR (Sloan et al, 2012b).…”

Section: Methodsmentioning

confidence: 99%

Rewiring of aminoacyl-tRNA synthetase localization and interactions in plants with extensive mitochondrial tRNA gene loss

Warren

Broz

Martinez-Hottovy

et al. 2022

Preprint

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The number of tRNAs encoded in plant mitogenomes varies considerably, with some lineages exhibiting rapid reductions. Loss of these bacterial-like mitochondrial tRNAs necessitates the import of nuclear-encoded counterparts that share little sequence similarity, raising questions about the identity and trafficking of enzymes necessary for the maturation and function of these newly imported tRNAs. In particular, the aminoacyl tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar or cytosolic tRNAs. Here, we investigated the evolution of aaRS subcellular localization in five species from a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion as well as scenarios where enzyme localization does not appear to change despite functional tRNA replacement. In most cases of transit peptide acquisition, the cytosolic enzyme gained a coding extension prior to the loss of the cognate mitochondrial tRNAs - suggesting a transitional state where organellar and cytosolic aaRSs colocalize to mitochondria. The ongoing functional replacement of Sileneae mitochondrial tRNAs and subsequent evolution of tRNA-interacting enzymes present an opportunity to study the coevolutionary dynamics of plant cytonuclear genetics.

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“…To identify Clp core subunit amino acid sequences, a custom Python script (https://github.com/alissawilliams/Gene_duplication_ACCase_Clp/scripts /local_blast5.py) was used to reciprocally blast (blastp v2.2.29) Arabidopsis thaliana amino acid sequences against predicted protein sequences from each of 22 other angiosperm species in the dataset. These 22 species were the same set used in Williams et al (2019) with the exclusion of Silene latifolia and Silene noctiflora, since Clp core subunit duplications have been previously studied in Sileneae (Rockenbach et al, 2016;Williams et al, 2021Williams et al, , 2019. This sampling was chosen to represent both the diversity of angiosperms and the range of rate variation in Clp complex evolution (Williams et al, 2019; see Table S3).…”

Section: Compilation and Curation Of Clp Core Subunit Amino Acid And Nucleotide Sequencesmentioning

confidence: 99%

“…These nine paralogs are the results of gene duplications throughout cyanobacterial and plastid evolution and are shared by all land plants (Olinares et al, 2011a). Ongoing gene duplication of individual subunits has been noted in a handful of angiosperm lineages (Rockenbach et al, 2016;Williams et al, 2021Williams et al, , 2019. Thus, the evolutionary trajectory of both of these essential plastid pathways is characterized by gene duplication at both ancient and recent timescales.…”

Section: Introductionmentioning

confidence: 99%

Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

Williams

Carter

Forsythe

et al. 2021

Preprint

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While the chloroplast (plastid) is known for its role in photosynthesis, it is also involved in many other biosynthetic pathways essential for plant survival. As such, plastids contain an extensive suite of enzymes required for non-photosynthetic processes. The evolution of the associated genes has been especially dynamic in flowering plants (angiosperms), including examples of gene duplication and extensive rate variation. We examined the role of ongoing gene duplication in two key plastid enzymes, the acetyl-CoA carboxylase (ACCase) and the caseinolytic protease (Clp), responsible for fatty acid biosynthesis and protein turnover, respectively. In plants, there are two ACCase complexes: a homomeric version present in the cytosol and a heteromeric version present in the plastid. Duplications of the nuclear-encoded homomeric ACCase gene and retargeting to the plastid have been previously reported in multiple species. We find that these retargeted copies of the homomeric ACCase gene exhibit elevated rates of sequence evolution, consistent with neofunctionalization and/or relaxation of selection. The plastid Clp complex catalytic core is composed of nine paralogous proteins that arose via ancient gene duplication in the cyanobacterial/plastid lineage. We show that further gene duplication occurred more recently in the nuclear-encoded core subunits of this complex, yielding additional paralogs in many species of angiosperms. Moreover, in six of eight cases, subunits that have undergone recent duplication display increased rates of sequence evolution relative to those that have remained single copy. We also compared rate patterns between pairs of Clp core paralogs to gain insight into post-duplication evolutionary routes. These results show that gene duplication and rate variation continue to shape the plastid proteome.

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Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

Cited by 10 publications

References 88 publications

New Geometric Models for Shape Quantification of the Dorsal View in Seeds of Silene Species

New Geometric Models for Shape Quantification of the Dorsal View in Seeds of Silene Species

Rewiring of aminoacyl-tRNA synthetase localization and interactions in plants with extensive mitochondrial tRNA gene loss

Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

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