DOI: 10.5061/dryad.n5tb2rbw3
title: Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas

description: Lianas, climbing woody plants, influence the structure and function of
 tropical forests. Climbing traits have evolved multiple times, including
 ancestral groups such as gymnosperms and pteridophytes, but the genetic
 basis of the liana strategy is largely unknown. Here, we use a comparative
 transcriptomic approach for 47 tropical plant species, including ten
 lianas of diverse taxonomic origins, to identify genes that are
 consistently expressed or downregulated only in lianas. Our comparative
 analysis of full-length transcripts enabled the identification of a core
 interactomic network common to lianas. Sets of transcripts identified from
 our analysis reveal features related to functional traits pertinent to
 leaf economics spectrum in lianas, including upregulation of genes
 controlling epidermal cuticular properties, cell wall remodeling, carbon
 concentrating mechanism, cell cycle progression, DNA repair and a large
 suit of downregulated transcription factors and enzymes involved in
 ABA-mediated stress response as well as lignin and suberin synthesis.
 Altogether, these genes are known to be significant in shaping plant
 morphologies through responses such as gravitropism, phyllotaxy and shade
 avoidance.
description: <strong><em>Sample
 Set</em></strong> The Luquillo
 transcriptomic set included six lianas (DIO) <em>Dioscorea
 poligonoides</em> (Dioscoreaceae), (HET) <em>Heteropterys
 laurifolia</em> (Malpighiaceae), (PAU) <em>Paulinia
 pinnata</em> (Sapindaceae), (SEC) <em>Securidaca
 virgata</em> (Polygonaceae), (SMI) <em>Smilax
 coriaceae</em> (Smilaceae), (DOL) <em>Dolichandra
 unguis-cati</em> (Bignoniaceae). We also included four more liana
 species from National Center for Biotechnology Information’s Sequence Read
 Archive (NCBI-SRA) and One Thousand Plant Genomes (1KP) dataset (Matasci
 et al. 2014, 1KP 2019) with the following accessions (GNE)
 <em>Gnetum montanum</em> (Gnetaceae) SRR5908685, (SMISIE)
 <em>Smilax sieboldii</em> (Smilacae) SRR5134200, (PASCAE)
 <em>Passiflora caerulea</em> (Passifloraceae) 1KP id:SIZE,
 (SCHPAR) <em>Schlegelia parasitica
 </em>(Schlegeliaceae) 1KP
 id:GAKQ. A full list including non-liana species can be found in the
 supplementary (<em>SI Appendix</em> Dataset S1, <em>SI
 Appendix</em> Fig. S1,).
 <strong><em>Sample Collection and RNA Library
 Construction</em></strong> To analyze the
 transcriptomes, we chose healthy and fully developed leaves from seedlings
 of tree and liana species distributed between 350 and 450 m in elevation
 from the Luquillo Experimental Forest (LEF) in the north eastern part of
 Puerto Rico. For each species, approximately 5 grams of leaf tissue was
 collected and placed in a 50 mL polypropylene conical tube with RNAlater
 (Thermo Fisher Scientific, Waltham, MA, USA). Explants were cut with a
 razor blade prior to being placed in the tube to allow the RNAlater to
 penetrate the mesophyll quickly. Samples were then frozen at -80ºC within
 two days. Rneasy Plant Mini Kit (Qiagen, Valencia, CA, USA) was used for
 RNA extraction. RNA quantification and quality metrics were carried out
 using a NanoDrop 2000 spectrophotometer (NanoDrop Products, Wilmington,
 DE, USA) and an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa
 Clara, CA, USA) RNAseq library preparations and sequencing were performed
 at the Beijing Genomics Institute, Shenzhen, China on Illumina Hiseq 2000
 sequencer generating 100 bp paired-end reads.
description: The dataset in this submission is in three parts:
 [1] A multi-tab Excel spreadsheet that includes species
 list; analysis results of QUAST quality control; validation of assembled
 transcriptomes by Bowtie2 alignments; measures of completeness by BUSCO
 analysis; results of gProfiler analysis for enriched genes, domains and
 categories. [2] A Cytoscape generated network used in
 Figure 1. For reproducible results we recommend selecting
 "Ripple" as the visual style and "Preset" as layout to
 retain formatting used in the manuscript. Source Cytoscape file
 (Liana-L5-L2.DRYAD.cys). [3] Four fasta formatted files
 for each species: (a) TRINITY assembled unfiltered
 transcripts (SPECIES.Trinity.fasta). (b) EnTAP filtered
 transcripts for non-plant contaminant sequences
 (SPECIES.decon.fasta).  (c) EnTAP filtered
 translated/frame-selected full-length protein sequences
 (SPECIES-fl-protein.fasta).  (d) EnTAP filtered
 full-length transcript nucleotide sequences
 (SPECIES-fl-nt.fasta).