Cotton Species

Diploids: A₂ and D₅

The Gossypium genus contains about 50 speciesWendel J F, Albert V A. Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications [J]. Syst Bot, 1992: 115-143.. Most of them are diploids and can be grouped to 8 diploid members (marked as A~G and K). They have different geographical origins and variable estimated genome sizes (Fig 1.)Hawkins J S, Kim H, Nason J D, et al. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium [J]. Genome Res, 2006, 16(10): 1252-1261., mostly due to different amount of DNA repeat elements. Despite all this, they share a common chromosome number (n = 13) and high levels of gene synteny.Rong J, Abbey C, Bowers J E, et al. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium) [J]. Genetics, 2004, 166(1): 389-417., indicating that they have a common ancestor (Fig 1.).

Tetraploids: AD₁ and AD₂

The tetraploid cotton species are thought to formed by an allopolyploidization event about 1~2 million years ago, which involved a D-genome species as the pollen-providing parent and an A-genome species as the maternal parentChen Z J, Scheffler B E, Dennis E, et al. Toward sequencing cotton (Gossypium) genomes [J]. Plant Physiol, 2007, 145(4): 1303-1310.(Fig 2.). Their descendants evolve into the current 5 tetraploid cotton species (Marked as AD₁~AD₅). Among them, the upland cotton G. hirsutum (AD₁) and sea-island cotton G. barbadense (AD₂) have become the main cultivated cotton species.

Please refer to CottonGen database to view all cotton species.

Fig 1. 8 diploid cotton members. Image from Hawkins et al 2006. Note the origin "New World" of D-subgenome refers to America.

Fig 2. Allopolyploidization leads to the current 5 tetraploid cotton species. The tetraploid AD_n genome sizes are roughly equal with the sum of genome sizes of A_n and D_n.

Genome Assembly

List of cotton genome assemblies.

Gene Models

Gene ID

Due to the limit of data providers, currently CottonFGD only includes protein coding genes.

All gene IDs are directly imported from data provider annotations. Therefore, you can directly use these IDs to search in other cotton databases (e.g., CottonGen). Their formats are listed as follows:

Transcript ID

IDs of transcripts are marked as .1, .2, .3, ..., appending to their gene IDs. IDs with .1 are usually the longest ones among all the isoforms (i.e., principle transcripts).

In order to maintain the consistence between the four cotton species, only principle transcripts are analyzed in CottonFGD.

Gene Name and Description

Each gene's name and description are based on its best homolog with Swiss-Prot proteins, as it is non-redundant and manually-reviewed. The homology is identified by NCBI BLAST+Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications [J]. BMC Bioinformatics, 2009, 10: 421.:

$ blastp -query [pep.fa] -db swissprotdb.fa -evalue 1e-5 -max_target_seqs 1 -max_hsps 1 

For each Swiss-Prot entry, the "Gene names" value is served as cotton gene's name (symbol) while the "Protein names" value is served as cotton gene's description. All genes with Swiss-Prot hits must have gene descriptions, but some of them have no gene names. For example, gene Gh_A01G0010 in G. hirsutum has its best Swiss-Prot homolog P48504. It has the description (Protein names) Cytochrome b-c1 complex subunit 6, but it has no gene names.

Transcript Structure

All the transcript structures: exons, introns, coding regions and untranslated regions (UTRs) are extracted from data providers annotations. It should be noticed that limited by data provider, UTR annotations might not completed.

Gene Function Annotation

As mentioned above, only the principle transcript of each gene is analyzed. Thus, all gene function annotations such as homology, GO(Gene Ontology), InterPro and pathway are all based on the protein sequences of their principle transcripts.

Protein Property Statistics

CottonFGD includes the following protein property statistics for each gene:

• Residue Composition:
  • The percentage of basic residues: His(H), Lys(K), Arg(R)
  • The percentage of acidic residues: Asp(D), Glu(E)
  All the remaining residues are neutral. Comparisons of the percentage of basic/acidic residues could give an rough estimation of protein's alkalinity or acidity.
• Molecular Weight (kDa)
• Charge
• Isoelectric Point: the pH value at which this molecule carries no net electrical charge
• Grand Average of Hydropathy: The sum of hydropathy values of all amino acids divided by the protein length. Positive value indicates hydrophobic.

The value of residue composition, molecular weight, charge and isoelectric point are calculated using pepstats in EMBOSS package (v6.5.7.0):

$ pepstats -sequence [pep.fa] -outfile [pep.out]

You can see an example of the output in the pepstats manual.

The value of Grand Average of Hydropathy is calculated using BioPerl (v1.6.924):

use Bio::SeqIO;
use Bio::Tools::SeqStats;   # Package to calculate hydropathicity
my $seqio_obj = Bio::SeqIO->new(-file=>shift, -format=>"fasta");
while (my $seq_obj = $seqio_obj->next_seq) {
    my $id = $seq_obj->display_id;
    my $seq_stats = Bio::Tools::SeqStats->new(-seq => $seq_obj);
    my $gravy;
    eval{$gravy = $seq_stats->hydropathicity();};
}

Protein Domain, Gene Ontology & InterPro Items

The possible domain regions for each protein and the associated GO (Gene Ontology) / InterPro items are predicted using a locally installed copy of InterProScan (v5.16-55.0):

./interproscan.sh -dp -f tsv -goterms -i [pep.fa]

Currently InterProScan includes 15 types of domain databases:

The accession ID formats of GO (Gene Ontology) and InterPro items are listed as follows:

Homology

Currently CottonFGD includes homology information for 22 other representative plant species from all the main categories: Eudicots, Monocots, Acrogymnospermae, Lycopodiidae, Bryophyta and Chlorophyta. Homology information are only available for genes in G. hirsutum, CRI assembly.

The best homolog for each cotton gene is searched using NCBI BLAST+, similar with defining gene names.

KEGG Pathway

The associated KEGG pathways for each gene is defined by two steps: First, all cotton genes are assigned to KEGG Orthology using the KEGG Automatic Annotation Server. We select all the available plant species as our "GENES data set". For each gene, only one KEGG Orthology item (ID Format: K[%05d]) is assigned. Then, the KEGG Orthology item is mapped to its associated KEGG Pathways (ID Format: map[%05d] or ko[%05d]) and KEGG Modules (ID Format: M[%05d])

Gene Expression

The expression patterns for each gene (i.e. principle transcript) are measured using RNA-seq datasets from SRP166405 Hu Y, Chen J, Fang L, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton[J]. Nature genetics, 2019, 51(4): 739-748.. This dataset contains 49 samples each with 1-3 biological replicates. Expression data are only available for genes in G. hirsutum, CRI assembly.

TPM values are calculated using salmon Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods. (v1.1.0).

salmon quant -i cDNA.Ghir.CRI -l A -1 reads.1.fq.gz -2 reads.2.fq.gz --seqBias --gcBias --validateMappings  -o output

The generated files quant.sf are available in the Download page.

Web Browser Compatibility

CottonFGD is designed to be compatible with all modern web browsers (such as Mozilla Firefox, Google Chrome, Sarifi, Microsoft Edge, etc ...) on a variety of devices (such as PC, tablet and mobile). Except for some subtle differences on front-end appearance, the recent version of Microsoft Internet Explorer (later than version 9.0) is also acceptable. It is strongly not recommended to use old versions of browsers (such as Internet Explorer lower than 8.0) as this would encounter many unnecessary bugs.

References