Pineapple Genomics Database

Data Information:

The Pineapple Genomics Database(PGD) combine different data sources for analyzing, such as genomic, transcriptomic, gene co-expression, molecular marker and comparative genomic data. Here, we described how the data was collected and how the analysis can be performed.

♦ Genomic Data

Table 1. Summary of genome assembly of pineapple variety 'F153' in PGD.

Assembly	Status	Number	N50 (kb)	Longest (kb)	size (Mb)	assembly(%)
Contigs	All	8986	126.5	1589.4	375.1	71.3
Scaffold	All	3133	11759.3	24880.7	381.9	72.6

Table 2. Summary of gene annotation of pineapple variety 'F153' in PGD.

Gene Annotation	Number	Percentage(%)
InterPro	12762	47.2%
KEGG Orthology	4229	15.6%
GO terms	6794	25.0%
Total annotated genes	13555	50.2%

♦ RNA-seq Data

Table 3. Summary of RNA-seq samples in PGD .

Species	Tissues	Collected
MD2	Leafs	Segment (S1-S6): 12:00, 22:00;White base/ Green tip: 10:00, 12:00, 13:00, 15:00, 16:00,18:00, 20:00, 22:00, 24:00, 2:00, 4:00, 6:00, and 8:00.
MD2	Fruits	Development stage1-6.
var.F153	Developing Flowers
var.F153	Roots

♦ Genetic Marker Data

Single nucleotide polymorphism (SNP): a total of 89 genome resequencing Ananas accessions were collected, and paired-end resequencing reads were mapped to the pineapple F153 reference genome.We identified 7,252,423 SNPs and 923,469 indels.

Simple sequence repeats (SSRs): a total of 4,629 CDS-SSR and 46,860 genomic-SSR markers were identified and made available in pineapple genome database with detailed information for the both types for users.

Intron polymorphism (IP): The PGD collected 17,540 IP loci, which are used to establish whether introns exist in the querying sequences using the IP development page.

♦ Gene-to-gene Co-expression

A total of 7228 informative genes (with FPKM greater than 5 in at least one tissue and a variance greater than 1) were obtained and gene pairs with absolute similarity of expression correlation greater than 0.65 were used as the final dataset. All datasets are easily navigable and available in PGD.

♦ Comparative Genomics Data

To clarify the evolutionary relationship and whole genome duplication (WGD) events between pineapple and other species (Oryza sativa, Vitis vinifera, Spirodela polyrhiza, Asparagus aofficinalis, Elaeis guineensis, Phoenix dactylifera, Sorghum bicolor and Musa acuminata ), we performed whole genome comparative analyses, and the collinear regions between pineapple and other species were grown out of MCscan25.