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The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes.

ABSTRACT: Premise of the study:The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods:Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. Results:Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. Discussion:Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.

SUBMITTER: Berger BA

PROVIDER: S-EPMC5664964 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes.

Berger Brent A BA Han Jiahong J Sessa Emily B EB Gardner Andrew G AG Shepherd Kelly A KA Ricigliano Vincent A VA Jabaily Rachel S RS Howarth Dianella G DG

Applications in plant sciences 20171020 10

<h4>Premise of the study</h4>The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae.<h4>Methods</h4>Twenty-four previ ...[more]

PMID: 29109919

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Project description:This paper provides a step-by-step guide for the morphological analysis of corolla and the decomposition of corolla shape variation into its symmetric and asymmetric components. The shape and symmetric organisation of corolla are key traits in the developmental and evolutionary biology of flowering plants. The various spatial layout of petals can exhibit bilateral symmetry, rotational symmetry or more complex combination of symmetry types. Here, I describe a general landmark-based geometric morphometric framework for the full statistical shape analysis of corolla and exemplify its use with four fully worked out case studies including tissue treatment, imaging, landmark data collection, file formatting, and statistical analyses: (i) bilateral symmetry (Fedia graciliflora), (ii) two perpendicular axes of bilateral symmetry (Erysimum mediohispanicum), (iii) rotational symmetry (Vinca minor), and (iv) combined bilateral and rotational symmetry (Trillium undulatum). The necessary tools for such analyses are not implemented in standard morphometric software and they are therefore provided here as functions running in the R environment. Principal Component Analysis is used to separate symmetric and asymmetric components of variation, respectively, quantifying variation among and within individuals. For bilaterally symmetric flowers, only one component of left-right asymmetric variation is extracted, while flowers with more complex symmetric layout have components of asymmetric variation associated with each symmetry operator implied (e.g., left-right asymmetry and adaxial-abaxial asymmetry). Fundamental information on the genetic, developmental, and environmental determinants of shape variation can be inferred from this decomposition (e.g., directional asymmetry, fluctuating asymmetry) and further exploited to document patterns of canalization, developmental stability, developmental modularity and morphological integration. Even if symmetry and asymmetry are not the primary interest of a study on corolla shape variation, statistical and anatomical arguments support the use of the framework advocated. This didactic protocol will help both morphometricians and non-morphometricians to further understand the role of symmetry in the development, variation and adaptive evolution of flowers.

Project description:Floral bilateral symmetry is one of the most important acquisitions in flower shape evolution in angiosperms. Members of Gesneriaceae possess predominantly zygomorphic flowers yet natural reversal to actinomorphy have independently evolved multiple times. The development of floral bilateral symmetry relies greatly on the gene CYCLOIDEA (CYC). Our reconstructed GCYC phylogeny indicated at least five GCYC duplication events occurred over the evolutionary history of Gesneriaceae. However, the patterns of GCYC expression following the duplications and the role of natural selection on GCYC copies in relation to floral symmetry remained largely unstudied. The Asiatic tribe Trichosporeae contains most reversals to actinomorphy. We thus investigated shifts in GCYC gene expression among selected zygomorphic species (Hemiboea bicornuta and Lysionotus pauciflorus) and species with reversals to actinomorphy (Conandron ramondioides) by RT-PCR. In the actinomorphic C. ramondioides, none of the three copies of GCYC was found expressed in petals implying that the reversal was a loss-of-function event. On the other hand, both zygomorphic species retained one GCYC1 copy that was expressed in the dorsal petals but each species utilized a different copy (GCYC1C for H. bicornuta and GCYC1D for L. pauciflorus). Together with previously published data, it appeared that GCYC1C and GCYC1D copies diversified their expression in a distinct species-specific pattern. To detect whether the selection signal (ω) changed before and after the duplication of GCYC1 in Asiatic Trichosporeae, we reconstructed a GCYC phylogeny using maximum likelihood and Bayesian inference algorithms and examined selection signals using PAML. The PAML analysis detected relaxation from selection right after the GCYC1 duplication (ωpre-duplication = 0.2819, ωpost-duplication = 0.3985) among Asiatic Trichosporeae species. We propose that the selection relaxation after the GCYC1 duplication created an "evolutionary window of flexibility" in which multiple copies were retained with randomly diverged roles for dorsal-specific expressions in association with floral symmetry changes.

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The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes.

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The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes.

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