Abstract
Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.
Abstract from the paper’s OpenAlex record; open copy licensed cc-by. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 13
Claim · model-written summary
The Tunisia pomegranate variety has softer seeds and big arils.
- Taxon
- pomegranate
Punica granatumt0 - Material
- 'Tunisia'e0
- Outcome
- softer seeds and big arilse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“The 'Tunisia' variety has softer seeds and big arils that are easily swallowed”
Claim · model-written summary
35.1 Gb of sequence data were acquired.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- data were acquirede0
- Value
- 35.1 Gbe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“A total of 35.1 Gb of data were acquired in this study”
Claim · model-written summary
The data included 280,881,106 raw reads.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- raw readse0
- Value
- 280,881,106e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“including 280,881,106 raw reads”
Claim · model-written summary
De novo assembly generated 132,287 transcripts.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- transcriptse0
- Value
- 132,287e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“de novo transcriptome assembly generated 132,287 transcripts”
Claim · model-written summary
Assembly yielded 105,743 representative unigenes.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- representative unigenese0
- Value
- 105,743e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“105,743 representative unigenes”
Claim · model-written summary
About 13,805 unigenes (37.7%) were longer than 1,000 bp.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- were longer than 1,000 bpe0
- Value
- 13,805 unigenes (37.7%)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“approximately 13,805 unigenes (37.7%) were longer than 1,000 bp”
Claim · model-written summary
A total of 76,806 unigenes were annotated.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- unigenes were annotatede0
- Value
- 76,806e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“a total of 76,806 unigenes were annotated”
Claim · model-written summary
72.63% of high-quality reads had at least one significant match to an existing gene model.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- significant match to an existing gene modele0
- Value
- 72.63%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“72.63% had at least one significant match to an existing gene model”
Claim · model-written summary
Seed formation in the two pomegranate cultivars involves lignin biosynthesis and metabolism, including genes encoding laccase, peroxidase, and WRKY, MYB and NAC transcription factors.
- Taxon
- pomegranatePunica granatume0
- Gene
- laccase and peroxidase, WRKY, MYB, and NAC transcription factorse0
- Outcome
- seed formatione0
- Qualifier
- lignin biosynthesis and metabolisme0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors”
Claim · model-written summary
Lignin-related and cellulose synthesis-related genes were highly expressed in hard-seed pomegranate.
- Taxon
- pomegranatePunica granatume0
- Material
- hard-seed pomegranatee0
- Outcome
- lignin-related genes and cellulose synthesis-related genese0
- Direction
- highly expressede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed”
Claim · model-written summary
Expression of genes related to flavonoids and programmed cell death was slightly higher in soft-seed pomegranates.
- Taxon
- pomegranatesPunica granatume0
- Material
- soft-seed pomegranatese0
- Outcome
- expression of genes related to flavonoids and programmed cell deathe0
- Direction
- slightly highere0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher”
Claim · model-written summary
Selected identified genes were validated by qRT-PCR.
- Taxon
- pomegranatePunica granatumt0
- Outcome
- validated selection of the identified genese0
- Qualifier
- qRT-PCRe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“pomegranate”
e0“We validated selection of the identified genes using qRT-PCR”
Claim · model-written summary
This is the first transcriptome analysis of Punica granatum.
- Taxon
- P. granatum L.Punica granatume0
- Outcome
- first transcriptome analysise0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“This is the first transcriptome analysis of P. granatum L.”