DOI: 10.5061/dryad.z08kprrpv
title: Full-length transcriptomes of 25 grassland plant species

description: Grasslands are essential, biodiverse ecosystems of economic importance
 that play a critical role for carbon storage and soil health. Despite
 their ecological and economic importance, transcriptomic resources for
 wild grassland species facilitating eco-evolutionary and functional
 genomic studies remain limited. In this study, we present full-length
 transcriptomes for shoot tissue of natural accessions of 25 wild grassland
 plant species collected from the field site of a long-term grassland
 biodiversity experiment (Jena Experiment). Using PacBio Iso-Seq
 technology, we generated a total of 522.45 million subreads which were
 assembled into isoforms for each species separately. This resulted in an
 average of 49,180 isoforms per species of which 68.6% were successfully
 annotated against the Swiss-Prot database. Fifty-six percent of the
 transcripts had complete open reading frames (ORFs), and 29.6% of the
 transcripts have been identified as non-coding RNAs (ncRNAs) by two
 prediction tools. This dataset provides a valuable full-length
 transcriptomic resource for exploring gene expression, alternative
 splicing, and evolutionary patterns in wild grassland plant species,
 paving the way for future functional genomics and conservation studies.
description: Substreads from PacBio Sequel II platform were processed using
 the PacBio Iso-Seq pipeline. Circular Consensus Sequences (CCS) were
 generated from subreads using the
 <strong><em>ccs</em></strong> tool (version 6.4.0)
 with default parameters, which identifies high-fidelity full-length reads
 by multiple passes of each molecule. These CCS reads were further
 processed with <strong><em>lima</em></strong>
 (version 2.9.0, using the <em>--isoseq</em> option) to remove
 sequencing adapters and barcodes. Poly(A) tails and artificial concatemers
 were removed using the
 <strong><em>isoseq</em></strong> tool (version
 4.0.0), yielding Full-Length Non-Chimeric (FLNC) reads. The FLNC reads
 were then clustered using <strong><em>isoseq
 cluster</em></strong> to generate polished isoforms, with the
 <em>--singletons</em> option enabled to retain singleton
 transcripts.
description: # Full-length transcriptomes of 25 grassland plant species
 [https://doi.org/10.5061/dryad.z08kprrpv](https://doi.org/10.5061/dryad.z08kprrpv) ## Description of the data and file structure This dataset contains 25 FASTA files, each representing the final assembled IsoSeq data for a grassland plant species. The respective file names listed below: | Species | Assembly | | :------------------------ | :------------------------------------------------- | | Lotus corniculatus | BMK230426-BJ202-01P0001.flnc.clustered.isoforms.fa | | Medicago variegata | BMK230426-BJ202-01P0002.flnc.clustered.isoforms.fa | | Trisetum flavescens | BMK230426-BJ202-01P0003.flnc.clustered.isoforms.fa | | Crepis biennis | BMK230426-BJ202-01P0004.flnc.clustered.isoforms.fa | | Geranium pratense | BMK230426-BJ202-01P0005.flnc.clustered.isoforms.fa | | Alopecurus pratensis | BMK230426-BJ202-01P0006.flnc.clustered.isoforms.fa | | Daucus carota | BMK230426-BJ202-01P0007.flnc.clustered.isoforms.fa | | Trifolium pratense | BMK230426-BJ202-01P0008.flnc.clustered.isoforms.fa | | Primula veris | BMK230426-BJ202-01P0009.flnc.clustered.isoforms.fa | | Knautia arvensis | BMK230426-BJ202-01P0010.flnc.clustered.isoforms.fa | | Ranunculus acris | BMK230426-BJ202-01P0011.flnc.clustered.isoforms.fa | | Plantago media | BMK230426-BJ202-01P0012.flnc.clustered.isoforms.fa | | Prunella vulgaris | BMK230426-BJ202-01P0013.flnc.clustered.isoforms.fa | | Plantago lanceolata | BMK230426-BJ202-01P0014.flnc.clustered.isoforms.fa | | Bellis perennis | BMK230426-BJ202-01P0015.flnc.clustered.isoforms.fa | | Veronica chamaedrys | BMK230426-BJ202-01P0016.flnc.clustered.isoforms.fa | | Holcus lanatus | BMK230426-BJ202-01P0017.flnc.clustered.isoforms.fa | | Lathyrus pratensis | BMK230426-BJ202-01P0018.flnc.clustered.isoforms.fa | | Luzula campestris | BMK230426-BJ202-01P0019.flnc.clustered.isoforms.fa | | Galium mollugo agg. | BMK230426-BJ202-01P0020.flnc.clustered.isoforms.fa | | Leucanthemum vulgare agg. | BMK230426-BJ202-01P0021.flnc.clustered.isoforms.fa | | Ajuga reptans | BMK230426-BJ202-01P0022.flnc.clustered.isoforms.fa | | Trifolium dubium | BMK230426-BJ202-01P0023.flnc.clustered.isoforms.fa | | Vicia cracca | BMK230426-BJ202-01P0024.flnc.clustered.isoforms.fa | | Arrhenatherum elatius | BMK230426-BJ202-01P0025.flnc.clustered.isoforms.fa | The plant samples were collected from the Jena Experiment, a long-term biodiversity experiment in a grassland ecosystem. Only shoot tissues were harvested for RNA extraction and sequencing. The sequencing was performed using the PacBio Sequel II platform. Circular Consensus Sequences (CCS) were generated from subreads using the ccs tool (version 6.4.0) with default parameters, which identifies high-fidelity full-length reads by multiple passes of each molecule. On average, 191,105 CCS reads were obtained per species (Table 1). These CCS reads were further processed with lima (version 2.9.0, using the *--isoseq* option) to remove sequencing adapters and barcodes. Poly(A) tails and artificial concatemers were removed using the isoseq tool (version 4.0.0), yielding Full-Length Non-Chimeric (FLNC) reads. The FLNC reads were then clustered using isoseq cluster to generate polished isoforms, with the *--singletons* option enabled to retain singleton transcripts. This dataset provides a valuable full-length transcriptomic resource for exploring gene expression, alternative splicing, and evolutionary patterns in wild grassland plant species, paving the way for future functional genomics and conservation studies. ### Files and variables #### File: BMK230426-BJ202-01P0024.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Vicia cracca #### File: BMK230426-BJ202-01P0025.flnc.clustered.isoforms.fa **Description:**  Final assembled IsoSeq data for Arrhenatherum elatius #### File: BMK230426-BJ202-01P0023.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Trifolium dubium #### File: BMK230426-BJ202-01P0022.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Ajuga reptans #### File: BMK230426-BJ202-01P0021.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Leucanthemum vulgare agg. #### File: BMK230426-BJ202-01P0020.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Galium mollugo agg. #### File: BMK230426-BJ202-01P0019.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Luzula campestris #### File: BMK230426-BJ202-01P0018.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Lathyrus pratensis #### File: BMK230426-BJ202-01P0017.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Holcus lanatus #### File: BMK230426-BJ202-01P0016.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Veronica chamaedrys #### File: BMK230426-BJ202-01P0015.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Bellis perennis #### File: BMK230426-BJ202-01P0013.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Prunella vulgaris #### File: BMK230426-BJ202-01P0014.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Plantago lanceolata #### File: BMK230426-BJ202-01P0012.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Plantago media #### File: BMK230426-BJ202-01P0011.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Ranunculus acris #### File: BMK230426-BJ202-01P0008.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Trifolium pratense #### File: BMK230426-BJ202-01P0010.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Knautia arvensis #### File: BMK230426-BJ202-01P0009.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Primula veris #### File: BMK230426-BJ202-01P0007.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Daucus carota #### File: BMK230426-BJ202-01P0005.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Geranium pratense #### File: BMK230426-BJ202-01P0004.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Crepis biennis #### File: BMK230426-BJ202-01P0006.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Alopecurus pratensis #### File: BMK230426-BJ202-01P0002.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Medicago variegata #### File: BMK230426-BJ202-01P0003.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Trisetum flavescens #### File: BMK230426-BJ202-01P0001.flnc.clustered.isoforms.fa **Description:** Final assembled IsoSeq data for Lotus corniculatus **Access information** Data was derived from the following sources: * Bioproject PRJNA1171640 on NCBI. (It specifies the raw data, and it will be released to public as soon as the manuscript is published).