⚙
AI-generated deep summary
by claude@2026-07, 2026-07-04
· read from full text
ⓘ
This bioinformatics study used public resequencing data from 36 Carica papaya individuals (24 males and 12 hermaphrodites) to perform a genotype–phenotype association analysis aimed at identifying genetic factors involved in papaya sex determination. Variants were called with BCFTOOLS (75,607 variants, reduced to 37,027 after filtering), then tested with PLINK and the 251 most significant variants were annotated with SnpEff, yielding 449 predicted effects, most classified as modifier-level impacts, and additional gene inferences were generated using Augustus and BLASTP along with comparisons between de novo assemblies of a male sample and alignment to the hermaphrodite sex-determining region. The authors explicitly frame these results as starting points for more robust mechanistic studies, implying limitations in the current data-driven inference. This paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.
Abstract
Papaya ( Carica papaya ) produces one of the most consumed fruits worldwide, holding great economic importance, especially in tropical regions. Papaya trade mainly involves gynodioecious cultivars with a ratio of 1:1 or 2:1 of hermaphrodites to females. For commercial reasons and also inherent to cultivation, it is preferable to have as many hermaphrodites as possible. In general, it is still not possible to produce only hermaphrodite seeds, so the sex of the plant is usually identified by conventional methods after the first flowering of the papaya plant. This occurs about 4-6 months after planting the seedling, with the females typically being discarded at the end. To avoid wasting resources and achieve higher harvest yields, producers may also resort to molecular methods using sex markers. However, this alternative also has its limitations, including high costs. Given these challenges, many researchers have focused on studying the process of sex determination in C. papaya , but the factors directly influencing this process remain unknown. The elucidation of this mechanism is not only of great agronomic interest, but also represents a significant opportunity for C. papaya to establish itself as a model organism for studying sexual chromosomes of recent evolutionary origin. Therefore, in this work, a bioinformatics strategy was used to address the topic. A genotype-phenotype association study was conducted to find possible genetic factors involved in sex determination using resequencing data from 36 individuals (24 male papaya plants and 12 hermaphrodites) obtained from public databases. The association study was preceded by a variant calling performed with BCFTOOLS, which found 75,607 variants, leaving 37,027 after filtering. Association studies were then carried out using the PLINK program with the filtered variants, and among these, 251 of the most statistically significant variants were applied to the SnpEff program for variant annotation, returning 449 effects, including 402 with a modifier level of impact, 22 with a low impact, and 25 with a moderate effect. Inferences and gene annotations were also performed using the Augustus software and BLASTP alignments with the gene sequences that had moderate effects predicted by SnpEff, as well as de novo genome assemblies of a male sample and its alignment with the hermaphrodite sex-determining region. These results were recorded and compared with previous studies in the literature. This allowed for the conclusion that the specific results obtained serve as a starting point for more robust studies to understand the molecular mechanisms of sex determination in C. papaya .
Full text
2,750 characters
· extracted from
oa-doi-fallback
· click to expand
Abstract
Papaya (Carica papaya) produces one of the most consumed fruits worldwide, holding great economic importance, especially in tropical regions. Papaya trade mainly involves gynodioecious cultivars with a ratio of 1:1 or 2:1 of hermaphrodites to females. For commercial reasons and also inherent to cultivation, it is preferable to have as many hermaphrodites as possible. In general, it is still not possible to produce only hermaphrodite seeds, so the sex of the plant is usually identified by conventional methods after the first flowering of the papaya plant. This occurs about 4-6 months after planting the seedling, with the females typically being discarded at the end. To avoid wasting resources and achieve higher harvest yields, producers may also resort to molecular methods using sex markers. However, this alternative also has its limitations, including high costs. Given these challenges, many researchers have focused on studying the process of sex determination in C. papaya, but the factors directly influencing this process remain unknown. The elucidation of this mechanism is not only of great agronomic interest, but also represents a significant opportunity for C. papaya to establish itself as a model organism for studying sexual chromosomes of recent evolutionary origin. Therefore, in this work, a bioinformatics strategy was used to address the topic. A genotype-phenotype association study was conducted to find possible genetic factors involved in sex determination using resequencing data from 36 individuals (24 male papaya plants and 12 hermaphrodites) obtained from public databases. The association study was preceded by a variant calling performed with BCFTOOLS, which found 75,607 variants, leaving 37,027 after filtering. Association studies were then carried out using the PLINK program with the filtered variants, and among these, 251 of the most statistically significant variants were applied to the SnpEff program for variant annotation, returning 449 effects, including 402 with a modifier level of impact, 22 with a low impact, and 25 with a moderate effect. Inferences and gene annotations were also performed using the Augustus software and BLASTP alignments with the gene sequences that had moderate effects predicted by SnpEff, as well as de novo genome assemblies of a male sample and its alignment with the hermaphrodite sex-determining region. These results were recorded and compared with previous studies in the literature. This allowed for the conclusion that the specific results obtained serve as a starting point for more robust studies to understand the molecular mechanisms of sex determination in C. papaya.
Competing Interest Statement
The authors have declared no competing interest.
Text is read by the "Ask this paper" AI Q&A widget below.
Extraction quality varies by source — PMC NXML preserves structure
cleanly, OA-HTML may include some navigation residue, and OA-PDF can
have broken hyphenation. The publisher copy
(via DOI)
is the canonical version.