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An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita.

Wyatt LE, Strickler SR, Mueller LA, Mazourek M - Hortic Res (2015)

Bottom Line: Comparison with the watermelon and cucumber genomes provided confirmation that the unigenes are full-length and comprehensive, covering an average of 90% of the coding sequence of their homologs and 72% of the cucumber and watermelon exomes.This transcriptome represents a major advance in C. pepo genomics, providing significant new sequence information and revealing the repertoire of genes expressed throughout winter squash fruit and seed development.Future studies on the genetic basis of fruit quality and future breeding efforts will be enhanced by tools and insights developed from this resource.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Breeding and Genetics, Cornell University , Ithaca, NY, USA.

ABSTRACT
Acorn squash (Cucurbita pepo) is an iconic fall vegetable in the United States, known for its unique fruit shape and also prized for its culinary properties. Little is known about the metabolism that underlies the development of fruit quality attributes such as color, sweetness, texture and nutritional qualities in acorn squash, or any other winter squash grown worldwide. To provide insight into winter squash fruit and seed development and add to the genomic resources in the Cucurbita genus, RNA sequencing was used to generate an acorn squash fruit and seed transcriptome from the cultivar Sweet REBA at critical points throughout fruit development. 141 838 600 high-quality paired-end Illumina reads were assembled into 55 949 unigenes. 85% of unigenes with predicted open reading frames had homology with previously identified genes and over 62% could be functionally annotated. Comparison with the watermelon and cucumber genomes provided confirmation that the unigenes are full-length and comprehensive, covering an average of 90% of the coding sequence of their homologs and 72% of the cucumber and watermelon exomes. Key candidate genes associated with carotenoid and carbohydrate metabolism were identified toward a resource for winter squash fruit quality trait dissection. This transcriptome represents a major advance in C. pepo genomics, providing significant new sequence information and revealing the repertoire of genes expressed throughout winter squash fruit and seed development. Future studies on the genetic basis of fruit quality and future breeding efforts will be enhanced by tools and insights developed from this resource.

No MeSH data available.


‘Sweet REBA’ acorn squash fruit at five developmental time points. Self-pollinated fruit were harvested at 5, 10, 15, 20 and 40 days after pollinations. Photos are of the interior and exterior of representative fruit at each time point.
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fig1: ‘Sweet REBA’ acorn squash fruit at five developmental time points. Self-pollinated fruit were harvested at 5, 10, 15, 20 and 40 days after pollinations. Photos are of the interior and exterior of representative fruit at each time point.

Mentions: RNA was extracted from fruit mesocarp and seed tissues of self-pollinated ‘Sweet REBA’ acorn squash fruit at 5, 10, 15, 20 and 40 days after pollination (Figure 1). All samples were pooled to create three biological replicates of a comprehensive fruit and seed sequencing library and paired-end reads were sequenced on one lane of an Illumina HiSeq 2000, resulting in a total of 156 540 465 pairs of 100 base pair (bp) reads (Table 1). After removing low-quality reads and trimming both adapter sequences and low-quality bases from the ends of reads, 141 838 600 paired reads remained, with an average length of 98.46 bp and an average quality score of 36.98, constituting a total of almost 28 Gbp of sequence (reads available in the NCBI Sequence Read Archive repository, run accession numbers SRR747836, SRR747920 and SRR747922). All sequence data were combined and assembled using the program Trinity35 to yield 161 780 contigs. These contigs were further assembled using the program iAssembler,36 which resulted in a total of 150 044 contigs. The contigs were then screened using the program DeconSeq37 to remove 2081 bacterial and mammalian sequence artifacts, leaving 147 963 unigenes with an average length of 1311 bp.


An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita.

Wyatt LE, Strickler SR, Mueller LA, Mazourek M - Hortic Res (2015)

‘Sweet REBA’ acorn squash fruit at five developmental time points. Self-pollinated fruit were harvested at 5, 10, 15, 20 and 40 days after pollinations. Photos are of the interior and exterior of representative fruit at each time point.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595981&req=5

fig1: ‘Sweet REBA’ acorn squash fruit at five developmental time points. Self-pollinated fruit were harvested at 5, 10, 15, 20 and 40 days after pollinations. Photos are of the interior and exterior of representative fruit at each time point.
Mentions: RNA was extracted from fruit mesocarp and seed tissues of self-pollinated ‘Sweet REBA’ acorn squash fruit at 5, 10, 15, 20 and 40 days after pollination (Figure 1). All samples were pooled to create three biological replicates of a comprehensive fruit and seed sequencing library and paired-end reads were sequenced on one lane of an Illumina HiSeq 2000, resulting in a total of 156 540 465 pairs of 100 base pair (bp) reads (Table 1). After removing low-quality reads and trimming both adapter sequences and low-quality bases from the ends of reads, 141 838 600 paired reads remained, with an average length of 98.46 bp and an average quality score of 36.98, constituting a total of almost 28 Gbp of sequence (reads available in the NCBI Sequence Read Archive repository, run accession numbers SRR747836, SRR747920 and SRR747922). All sequence data were combined and assembled using the program Trinity35 to yield 161 780 contigs. These contigs were further assembled using the program iAssembler,36 which resulted in a total of 150 044 contigs. The contigs were then screened using the program DeconSeq37 to remove 2081 bacterial and mammalian sequence artifacts, leaving 147 963 unigenes with an average length of 1311 bp.

Bottom Line: Comparison with the watermelon and cucumber genomes provided confirmation that the unigenes are full-length and comprehensive, covering an average of 90% of the coding sequence of their homologs and 72% of the cucumber and watermelon exomes.This transcriptome represents a major advance in C. pepo genomics, providing significant new sequence information and revealing the repertoire of genes expressed throughout winter squash fruit and seed development.Future studies on the genetic basis of fruit quality and future breeding efforts will be enhanced by tools and insights developed from this resource.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Breeding and Genetics, Cornell University , Ithaca, NY, USA.

ABSTRACT
Acorn squash (Cucurbita pepo) is an iconic fall vegetable in the United States, known for its unique fruit shape and also prized for its culinary properties. Little is known about the metabolism that underlies the development of fruit quality attributes such as color, sweetness, texture and nutritional qualities in acorn squash, or any other winter squash grown worldwide. To provide insight into winter squash fruit and seed development and add to the genomic resources in the Cucurbita genus, RNA sequencing was used to generate an acorn squash fruit and seed transcriptome from the cultivar Sweet REBA at critical points throughout fruit development. 141 838 600 high-quality paired-end Illumina reads were assembled into 55 949 unigenes. 85% of unigenes with predicted open reading frames had homology with previously identified genes and over 62% could be functionally annotated. Comparison with the watermelon and cucumber genomes provided confirmation that the unigenes are full-length and comprehensive, covering an average of 90% of the coding sequence of their homologs and 72% of the cucumber and watermelon exomes. Key candidate genes associated with carotenoid and carbohydrate metabolism were identified toward a resource for winter squash fruit quality trait dissection. This transcriptome represents a major advance in C. pepo genomics, providing significant new sequence information and revealing the repertoire of genes expressed throughout winter squash fruit and seed development. Future studies on the genetic basis of fruit quality and future breeding efforts will be enhanced by tools and insights developed from this resource.

No MeSH data available.