**2. Classification**

Papaya is a member of the Family Caricaceae of which there are six genera *Carica*, *Jarilla*, *Horovitzia*, *Jacaratia*, *Vasconcella*, and *Cylicomorpha*. Papaya is a member of the Genus *Carica* of which there is only one species, *Carica papaya*. There are a total of 35 species in the Family Caricaceae; *Carica* (one), *Jarilla* (three), *Horovitzia* (one), *Jacaratia* (eight), *Vasconcella* (20), and *Cylicomorpha* (two). Although papaya is the

only well-known edible fruit, other genera such as *Vasconcellea* (also called mountain papaya), *Jarilla* and *Jacaratia* are also consumed as fruit in Central America [3]. With the exception of the Genus *Cylicomorpha* which is native to Africa, all are native to the Americas.

#### **2.1 Morphology and general characters**

Plants in the family Caricaceae are stout-stemmed trees and exudate latex-like substances. Their leaves are palmately compound or lobed. The inflorescences are axillary and cymose and the flowers usually have fused petals. The fruits consist of numerous seeds surrounded by mucilage [11]. Of all the species in the family Caricaceae, papaya (*Carica papaya*) is the most well-known species ostensibly due to its fruit. Papaya is known by various names including pawpaw (Australia), Malagor (Thailand), tree melon (Brazil), and Fruitabomba (Cuba) [12]. Papaya is a herbaceous plant and, depending on the variety of which there are many, grows to a height of up to ten meters in height. The leaves are palmately-lobed with long and hollow petioles and the blades are divided into 5–9 segments. The flower buds are developed at the axils of the leaves. The fertilized fruit consists of up to 1000 seeds. The fruit skin is green at the unripened stage and turns yellow-orange when ripens. Generally, papaya plants have a life span of between five and ten years [13].

Most species in the family Caricaceae are dioecious. One is monoecious and two, *C. papaya* and *V. cundimarsensis* are trioecious [14]. Although the morphology of male, female and hermaphrodite papaya plants are very similar, their flowers and fruits were distinct. The male papaya plants produce small flowers in clusters with long peduncles and produce no or very small fruits. The female plants have large and round flowers while the fruits are round or ovule. The hermaphrodite flowers are cylindrical and produce cylindrical fruits. The fruits from hermaphrodite papaya have superior quality (size, shape, and flesh thickness) than those from female papaya plants. Based on fruit types, papaya cultivars can be divided into Solo and Formosa types. The fruits from the Solo group are small (500–700 g) with oval or pear shape, while those of the Formosa group are medium to large (≥1000 g) with cylindrical shape [15].

#### **2.2 Genomics**

Papaya (*Carica papaya*) has a relatively small genome of approximately 372 Mb across 18 chromosomes (2n = 2x = 18). Papaya chromosomes consist of autosomes and sex chromosomes. Male papaya has the sex chromosome XY and female XX, while the hermaphrodite papaya has XY<sup>h</sup> . The nucleotide composition of the papaya genome is typical of dicot plants with a GC content of 36.51% GC and AT content of 63.49% [16]. The draft genomic sequence of a genetically modified variety of the female papaya, "SunUp", which was derived from the Hawaiian inbred cultivar "Sunset", was published in 2008 [17].

#### *2.2.1 Sex determination*

The papaya Y-chromosome deviated from the X-chromosome through deletions. Male-specific regions accounted for approximately 13% of Y-chromosome and share 99.6% of identity in male (MSY) and hermaphrodite (HSY) papaya [18, 19]. It consists of four knobs like heterochromatic structure and is heavily methylated

[18]. Expression of genes linked to X, Y and Yh chromosomes showed evidence of partial dosage compensation in X-link loci and a candidate gene associated with papaya sex determination and the transition to hermaphroditism, a homolog of the MADS-box protein short vegetative phase (SVG) [20, 21]. The dosage compensation of gene expression in papaya sex chromosomes was investigated further in female and male papaya and found to be at a gene by gene level. In addition, expression of most X-hemizygous genes was very low or none suggesting the role of gene silencing in controlling of transcriptional balance [22]. Recently, the landscapes of DNA methylation and transcriptomes were shown to be different in male and female papaya [23].

Using sequence information derived from papaya sex chromosomes, sex-specific primers were designed and used to screen plantlets/seedlings to identify fruit-bearing female and hermaphrodite types from males (MSY) [24]. More recently, a candidate gene, monodehydroascorbate reductase 4 (MDAR4), was identified from H-TSS No.7 line with X-chromosome mutant (3 bp deletion) resulting in all hermaphrodite progeny. MDAR4 is involved in a hydrogen peroxide scavenging pathway [25]. The marker developed from this gene has potential applications in papaya breeding, selection of potential lines for in vitro clonal propagation, and the production of high-quality commercial varieties of papaya seedlings.

#### **2.3 Agronomic characteristics**

Target genes related to papaya's important agronomic traits, including tolerance/ resistance to abiotic and biotic stresses and fruit quality, were explored through omics and bioinformatics [26]. The papaya genome includes NBS genes which are diseaseresistant genes with nucleotide-binding site motifs in the Toll/interleukin-1 receptor (TIR) and non-TIR subclasses [27]. Transcriptome profiles in young leaves of papaya ringspot virus (PRSV) resistant genetically modified variety "Sunup" showed high expression of several transcription factors (TFs) including MYB, ERF, WRKY, NAC, transporter proteins, and hormone-related proteins compared to susceptible "Sunset" papaya plants [28]. Under mild drought stress, stress-responsive genes were differentially expressed in papaya tissues with genes related to cell cycle and DNA repair processes. These stress-responsive genes were up-regulated in papaya leaves and sap while genes related to hormone signaling and sucrose metabolism were up-regulated in roots. Under severe drought stress genes related to oxidation-reduction, abiotic stress responses, and hormone signaling were also found to be up-regulated in all tissues [29]. Drought tolerant papaya had more photosynthetic II (PSII) efficiency than susceptible papaya. Drought susceptible plants displayed greater leaf abscission, less turgid shoots, and lower plant growth than those of tolerant papaya. Molecular analysis identified six transcription factors including *CpHSF*, *CpMYB*, *CpNAC*, *CpNFY-A*, *CpERF*, and *CpWRKY* that were highly expressed in tolerant papaya [30]. These genes were reportedly also involved in drought tolerance in rice and maize [31, 32]. Two transcription factors, RAP2.4 and DREB2 belonging to the ethylene response AP2/ERF family, have also been linked to extreme temperature responses in papaya. Overexpression of these genes in transformed tobaccos resulted in the cold (4°C) and heat tolerance (40°C) [33, 34]. In the regulation of fruit development and ripening, the papaya SQUAMOSA promoter binding protein Cp-SPL was found to be differentially expressed and cpmiRNA156 appears to play a critical role [35]. While in the carotenoid biosynthetic pathway, critical in the color development of papaya fruit, transcription factors HLH1 and HLH2 appear to regulate the transcription of lycopene β-cyclase genes [36].
