Dataset Information

Data on vegetation sampling in areas dominated by Pteridium aquilinum in Nyungwe forest, Western Province of Rwanda.

ABSTRACT: The data presented in this article describe plant traits (ecological strategy, plant succession, biological form, plant distribution and conservation status), cover-abundance scores of individualized communities after the application of Multivariate Statistical Package (MVSP) software and coverage percentage of species which compose the communities in areas sampled from Nyungwe forest. Taxonomic diversity indices (Shannon, Evenness and Richness) were also calculated and included in the dataset. The observed data can support the evaluation of Pteridium invasion in comparable forest types.

SUBMITTER: Senyanzobe JMV

PROVIDER: S-EPMC7829135 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Data on vegetation sampling in areas dominated <i>by Pteridium aquilinum</i> in Nyungwe forest, Western Province of Rwanda.

Senyanzobe J M V JMV Mulei Josephine M JM Bizuru Elias E Nsengumuremyi Concorde C

Data in brief 20210118

The data presented in this article describe plant traits (ecological strategy, plant succession, biological form, plant distribution and conservation status), cover-abundance scores of individualized communities after the application of Multivariate Statistical Package (MVSP) software and coverage percentage of species which compose the communities in areas sampled from Nyungwe forest. Taxonomic diversity indices (Shannon, Evenness and Richness) were also calculated and included in the dataset. ...[more]

PMID: 33532529

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Project description:Considerable areas dominated by bracken Pteridium aquilinum (L.) Kuhn occur worldwide and are associated with arrested forest recovery. How forest recovery is impeded in these areas remains poorly understood, especially in the African highlands. The component processes that can lead to recruitment limitation-including low seed arrival, availability and persistence-are important determinants of plant communities and offer a potential explanation for bracken persistence. We investigated key processes that can contribute to recruitment limitation in bracken-dominated clearings in the Bwindi Impenetrable National Park, Uganda. We examined if differences in seed rain (dispersal limitation), soil seed bank, or seed removal (seed viability and persistence) can, individually or in combination, explain the differences in tree regeneration found between bracken-dominated areas and the neighboring forest. These processes were assessed along ten 50-m transects crossing the forest-bracken boundary. When compared to the neighboring forest, bracken clearings had fewer seedlings (bracken 11,557 ± 5482 vs. forest 34,515 ± 6066 seedlings/ha), lower seed rain (949 ± 582 vs. 1605 ± 335 tree seeds m-2 year-1), comparable but sparse soil seed bank (304 ± 236 vs. 264 ± 99 viable tree seeds/m2), higher seed removal (70.1% ± 2.4% vs. 40.6% ± 2.4% over a 3-day interval), and markedly higher rodent densities (25.7 ± 5.4 vs. 5.0 ± 1.6 rodents per 100 trapping sessions). Camera traps revealed that rodents were the dominant animals visiting the seeds in our seed removal study. Synthesis: Recruitment limitation contributes to both the slow recovery of forest in bracken-dominated areas, and to the composition of the tree species that occur. Low seed arrival and low persistence of unburied seeds can both explain the reduced density of seedlings found in bracken versus neighboring forest. Seed removal, likely due to rodents, in particular appears sufficient to constrain forest recovery and impacts some species more severely than others.

Project description:BackgroundBecause of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies.Results681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled de novo into 56,256 unique sequences (i.e. unigenes) with a mean length of 547.2 bp and a total assembly size of 30.8 Mbp with an average read-depth coverage of 7.0×. We estimate that 87% of the complete transcriptome has been sequenced and that all transcripts have been tagged. 61.8% of the unigenes had blastx hits in the NCBI nr protein database, representing 22,596 unique best hits. The longest open reading frame in 52.2% of the unigenes had positive domain matches in InterProScan searches. We assigned 46.2% of the unigenes with a GO functional annotation and 16.0% with an enzyme code annotation. Enzyme codes were used to retrieve and color KEGG pathway maps. A comparative genomics approach revealed a substantial proportion of genes expressed in bracken gametophytes to be shared across the genomes of Arabidopsis, Selaginella and Physcomitrella, and identified a substantial number of potentially novel fern genes. By comparing the list of Arabidopsis genes identified by blast with a list of gametophyte-specific Arabidopsis genes taken from the literature, we identified a set of potentially conserved gametophyte specific genes. We screened unigenes for repetitive sequences to identify 548 potentially-amplifiable simple sequence repeat loci and 689 expressed transposable elements.ConclusionsThis study is the first comprehensive transcriptome analysis for a fern and represents an important scientific resource for comparative evolutionary and functional genomics studies in land plants. We demonstrate the utility of high-throughput sequencing of a normalized cDNA library for de novo transcriptome characterization and gene discovery in a non-model plant.

Dataset Information

Data on vegetation sampling in areas dominated by Pteridium aquilinum in Nyungwe forest, Western Province of Rwanda.

Publications

Data on vegetation sampling in areas dominated <i>by Pteridium aquilinum</i> in Nyungwe forest, Western Province of Rwanda.

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