DOI: 10.5061/dryad.256hn
title: Data from: Insights into the ecology and evolution of polyploid plants through network analysis

description: Polyploidy is a widespread phenomenon throughout eukaryotes, with
 important ecological and evolutionary consequences. Although genes operate
 as components of complex pathways and networks, polyploid changes in genes
 and gene expression have typically been evaluated as either individual
 genes or as a part of broad-scale analyses. Network analysis has been
 fruitful in associating genomic and other 'omic'-based changes
 with phenotype for many systems. In polyploid species, network analysis
 has the potential not only to facilitate a better understanding of the
 complex 'omic' underpinnings of phenotypic and ecological traits
 common to polyploidy, but also to provide novel insight into the
 interaction among duplicated genes and genomes. This adds perspective to
 the global patterns of expression (and other 'omic') change that
 accompany polyploidy and to the patterns of recruitment and/or loss of
 genes following polyploidization. While network analysis in polyploid
 species faces challenges common to other analyses of duplicated genomes,
 present technologies combined with thoughtful experimental design provide
 a powerful system to explore polyploid evolution. Here, we demonstrate the
 utility and potential of network analysis to questions pertaining to
 polyploidy with an example involving evolution of the transgressively
 superior cotton fibres found in polyploid Gossypium hirsutum. By combining
 network analysis with prior knowledge, we provide further insights into
 the role of profilins in fibre domestication and exemplify the potential
 for network analysis in polyploid species.
description: Ghirsutum_CRB252_5dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gzGhir-CRB252_5dpa_ATTCCT.fastq.gzGhirsutum_CRB252_10dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gzGhir-CRB252_10dpa_CAGATC.fastq.gzGhirsutum_CRB252_15dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gzGhir-CRB252_15dpa_GGCTAC.fastq.gzGhirsutum_CRB252_20dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gzGhir-CRB252_20dpa_ACAGTG.fastq.gzGhirsutum_Maxxa_5dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Maxxa_5dpa_ACTTGA.fastq.gzGhirsutum_Maxxa_10dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Maxxa_10dpa_CAGATC.fastq.gzGhirsutum_Maxxa_15dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Maxxa_15dpa_AGTTCC.fastq.gzGhirsutum_Maxxa_20dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Maxxa_20dpa_GTGAAA.fastq.gzGhirsutum_TM1_5dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gzGhir-TM1_5dpa_ACTGAT.fastq.gzGhirsutum_TM1_10dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gzGhir-TM1_10dpa_GTCCGC.fastq.gzGhirsutum_TM1_15dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gzGhir-TM1_15dpa_GTGGCC.fastq.gzGhirsutum_TM1_20dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gzGhir-TM1_20dpa_GTGAAA.fastq.gzGhirsutum_TX665_5dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx665_5dpa_CTTGTA.fastq.gzGhirsutum_TX665_10dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx665_10dpa_CGATGT.fastq.gzGhirsutum_TX665_15dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx665_15dpa_TAGCTT.fastq.gzGhirsutum_TX665_20dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx665_20dpa_GTTTCG.fastq.gzGhirsutum_TX2095_5dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx2095_5dpa_AGTCAA.fastq.gzGhirsutum_TX2095_10dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx2095_10dpa_TGACCA.fastq.gzGhirsutum_TX2095_15dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx2095_15dpa_GAGTGG.fastq.gzGhirsutum_TX2095_20dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Tx2095_20dpa_CGTACG.fastq.gzGhirsutum_yuc_5dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Yuc_5dpa_TAGCTT.fastq.gzGhirsutum_yuc_10dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Yuc_10_AGTTCC.fastq.gzGhirsutum_yuc_15dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Yuc_15dpa_GATCAG.fastq.gzGhirsutum_yuc_20dpaIllumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gzGhir-Yuc_20dpa_CCGTCC.fastq.gz