Dataset Information

Identification and Molecular analysis of the Y-specific CpMp gene controlling long male peduncles in papaya

ABSTRACT:

Papaya is a fruit crop possessing XY sex chromosomes. The development of long

male peduncles (Mp) is pivotal for the evolutionary transition from gynodioecy to

dioecy. The gene, CpMp, which controls peduncle length, is one of the four genes

contributing to the evolution of stage 3 sex chromosomes in papaya. We identified a

Y-specific SVP paralog, CpSVP-Yp, as a candidate gene for CpMp through

comparative genomic analyses and functional validation by complementation tests.

CpMp promotes peduncle elongation by directly activating CpYUC6, an auxin

biosynthesis gene, thereby increasing IAA levels. Elevated IAA in turn enhance GA,

triggering expression of the GA stimulated gene CpGASA6, which drives cell division

and elongation. Overexpression CpGASA6 confirmed its role in peduncle growth but

revealed a feedback inhibition on IAA biosynthesis. Two upstream regulators of

CpMp were identified, CpTRAB1, a positive regulator repressed by GA, and

CpGATA8, a negative regulator upregulated by CpMp, forming two feedback loops.

Notably, male trees produce 400 times more pollen than hermaphrodites, offering a

clear fitness advantage. In papaya, three genes - two sex determination genes and this

long male peduncle gene, are essential for the establishment of dioecy and the

initiation of sex chromosome evolution. These findings fill a major gap in

understanding papaya sex chromosome evolution and offer valuable genetic resources

for papaya improvement.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

PROVIDER: MTBLS13183 | MetaboLights | 2025-10-20

REPOSITORIES: MetaboLights

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Source:

			Action	DRS
	a_MTBLS13183_LC-MS_negative_reverse-phase_metabolite_profiling.txt	Txt
	a_MTBLS13183_LC-MS_positive_reverse-phase_metabolite_profiling.txt	Txt
	i_Investigation.txt	Txt
	m_MTBLS13183_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsv	Tabular
	m_MTBLS13183_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv	Tabular

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Project description:CLAMP transcription factor is a GA binding protein that recruits the male dosage compensation complex MSL to male X-chromosome, thus upregulating transcription level twice that of female X-chromosomes. Interestingly, CLAMP is essential for survival of both male and female individuals. However, what function it plays at the autosomes, especially in females is not known. It is well establised that GA-rich sequences to which CLAMP bind have evolved from polypyrimidine tracts that regulate splicing. Also, MALDI-MS data shows that CLAMP binds to RNA binding proteins involved in sex-specific splicing like, Squid. Furthermore, as part of MSL complex CLAMP interacts with MLE, a RNA helicase which is a known component of spliceosome complex conserved from flies to humans. Thus, we hypothesized that CLAMP plays a role in sex-spcific splicing. Given that CLAMP is a transcription factor, understanding mechanism of how it regulates splicing will add to our understanding about how regulators of gene expression shape the transcriptome differentially between males and females. We tested our hypothesis by identifying CLAMP dependent female and male sex-specific splicing events by analysing RNA-seq data from control as well as clampnull mutant male and female third instar larvae (L3) using suppa based time2splice pipeline (https://github.com/ashleymaeconard/time2splice). We identified 189 and 211 CLAMP dependent splicing events in female and male L3. Out of these 139 were female sex-specific splicing whereas 161 was male-sex-specific splicing. 50 splicing events identified as CLAMP dependent were non-specific to any particular sex, and were affect in both the sexes. Interestingly, we identified splicing of master regulator of sex-determination sxl affected by absence of CLAMP in females whereas splicing of one of the sex-determination pathway effectors, tra regulated by CLAMP in males. These findings indicate CLAMP plays important role in determining sex-specific transcript diversity in Drosophila.

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Identification and Molecular analysis of the Y-specific CpMp gene controlling long male peduncles in papaya

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