Skip to main content

Java apple (Syzygium samarangense) genome reveals evolution of fruit size, sweetness and seedlessness

Dlium Java apple (Syzygium samarangense) genome reveals evolution of fruit size, sweetness and seedlessness

NEWS - Researchers have successfully decoded the autotetraploid genome of wax apple or java apple (Syzygium samarangense) revealing the genetic evolution and key factors driving fruit diversity. The study highlights a rich antioxidant profile that promises health benefits and breeding strategies to improve nutritional value.

S. samarangense, with its crisp texture, fresh aroma and health benefits, faces breeding challenges due to complex genetic diversity and limited genomic data. These constraints have hampered efforts to improve fruit qualities such as size and sugar content.

The researchers identified 344 single-copy genes from 12 genomes sequenced using OrthoFinder and then used them to construct a phylogenetic tree. S. samarangense, Eucalyptus grandis, Psidium guajava, Rhodomyrtus tomentosa and Punica granatum belong to the same branch of Myrtales. The divergence of Myrtales occurred 79.4 million years ago.

A much closer genetic relationship was observed between S. samarangense and E. grandis. The two species diverged from each other 26 million years ago. CAFÉ analysis characterized 1328 expanded gene families and 5363 reduced gene families.

Gene Ontology (GO) enrichment analysis showed that the 1328 expanded gene families were mainly enriched in DNA polymerase activity, nucleocapsid retrotransposons and mitochondrial fission. In contrast, 5363 gene families were mainly enriched in serine/threonine kinase protein activity, flower organ senescence, and secondary metabolite biosynthesis processes.

Compared with other species, 537 unique gene families were identified in the S. samarangense genome. These gene families were mainly enriched in a series of functional items, including catalytic activities acting on DNA, retrotransfer, nucleocapsid, transfer, and mediated RNA.

Comparison among the four haplotypes revealed 4.53 million SNPs, 0.49 million short indels, and 10,925 structural variations (SVs). These genetic variations were evenly distributed along the 44 chromosomes. Chromosome-specific 13-mer clustering divided each set of four haplotypes together which was inconsistent with the allotetraploid Miscanthus genome and showed separate subgenome distributions. Smudge plot analysis identified the AAAB pattern as the dominant component accounting for 56% of the examined K-mers.

These results collectively indicate that S. samarangense has an autotetraploid genome with a high degree of heterozygosity. The distribution of synonymous substitutions per synonymous site (Ks) of homologous gene pairs clearly illustrates that the S. samarangense genome has undergone three rounds (WGT-γ, WGD-1, and WGD-2) of whole genome duplication events.

In addition to WGT-γ which is common in the evolutionary history of grape and E. grandis, researchers found that S. samarangense and E. grandis have also undergone an independent whole genome duplication (WGD-1). Compared with the situation in E. grandis, the specific WGD-1 event that occurred in the S. samarangense genome is more complex.

In addition, the synteny relationship between S. samarangense and Vitis vinifera was further analyzed to verify that WGD-1 and WGD-2 occurred after WGT-γ. The collinearity relationship between S. samarangense and V. vinifera was 8:1, indicating the occurrence of two lineage-specific WGDs in S. samarangense.

The research team published chromosome-scale genome and transcriptome data of the species with a focus on genes regulating size, sugar metabolism and male sterility. The findings open up new possibilities for molecular breeding of varieties.

The 1.59 Gb genome reveals three rounds of genome duplication events. Key genes influencing fruit size, including APETALA1 (AP1) and APETALA1 (AP2), drive growth by regulating sepal development. Sweetness has been associated with the expression of sugar transporter genes such as Sugars Will Finally be Exported Transporters (SWEETS) and Sucrose Transporters (SUTs).

Male sterility is a result of the lack of expression of genes such as DYSFUNCTIONAL TAPETUM1 (DYT1), TAPETUM DEVELOPMENT AND FUNCTION1 (TDF1), and ABORTED MICROSPORE (AMS) which are essential for tapetum development and pollen viability. Male sterility contributes to seedless fruit formation, a highly valued trait in the market.

“This is a major advance in understanding the genetic basis of these important fruit traits. The genomic haplotypes are an important resource for exploring genetic diversity and selective breeding to create superior varieties with improved size, sweetness and seedlessness,” said Lihui Zeng from Fujian Agriculture and Forestry University.

This research can accelerate breeding programs focused on developing wax apples with improved fruit size, higher sugar content and seedlessness traits that are in line with consumer demand. These findings also provide a valuable framework for improving other fruits facing breeding challenges and strides in the field of horticultural genomics.

Original research

Xiuqing Wei, Min Chen, Xijuan Zhang, Yinghao Wang, Liang Li, Ling Xu, Huanhuan Wang, Mengwei Jiang, Caihui Wang, Lihui Zeng, Jiahui Xu, The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple (Syzygium samarangense (Blume) Merr. and Perry), Horticulture Research, Volume 10, Issue 12, December 2023, uhad214, DOI:10.1093/hr/uhad21

Dlium theDlium

Popular Posts

Indian shot (Canna indica)

Puspa midra or Indian shot ( Canna indica ) is is plant species in Cannaceae, annual, shrub 0.5-2.5 meters high, depending on variety, erect stems, unbranched and leaf midrib arranged overlapping to form pseudostems and hermaphrodite flowers. C. indica forms a branched rhizome, 60 cm long which is divided into rounded segments and is covered in two stripes by pale green or purple scaly leaves. The rhizome has tubers that contain very large starch grains. The surface has transverse furrows, the underside appears white roots and numerous shoots. The leaves sit alternate and spiral or arranged in two rows, very large and divided into a leaf midrib, short stalk and blade. The strands are 30-60 cm long, 10-20 cm wide and have linear veins, green or purple-green, the base blunt or narrowly pointed and the apex immediately tapering or sharp. Hermaphrodite flowers, pedicels 0.2-1 cm long and red or yellow-orange, except in some cultivars 4.5-7.5 cm long. The sepals are triangular in shape a...

Guinea grass (Panicum maximum)

Guinea grass or buffalo grass or green panic ( Panicum maximum ) is a plant species in Poaceae, annual grasses, growing upright to form clumps, strong, cultivated in all tropical and subtropical regions for very high value as fodder. P. maximum reproduces in very large pols, fibrous roots penetrate into the soil, upright stems, green, 1-1.5 m tall and have smooth cavities for diameters up to 2.5 mm. Propagation is done vegetatively and generatively. Ribbon-shaped leaves with a pointed tip, very many, built in lines, green, 40-105 cm long, 10-30 mm wide, erect, branched, a white linear bone, often covered with a layer of white wax, rough surface by hair short, dense and spread. The flower grows at the end of a long and upright stalk, open with the main axis length to more than 25 cm and the length of the bunches down to 20 cm. Grains have a size of 3x4 mm and oval. Seeds have a length of 2.25-2.50 mm and each 1 kg contains 1.2 - 1.5 million seeds. Guinea grass has two varieties. P...

Indian rosewood (Dalbergia latifolia)

Sonokeling or Java palisandre or Indian rosewood ( Dalbergia latifolia ) is a species of plant in the Fabaceae, a large tree producing hardwood, medium weight and high quality, rounded leaves, thin and broad pods, highly adaptive, grows in dry and rocky landscapes with lots of sunlight. D. latifolia has medium to large size, cylindrical stems, up to 40 m high with a ring of up to 2 m, the bark is brownish gray and slightly cracked longitudinally. The crown is dense, dome-shaped and sheds leaves. The leaves are compound and pinnate oddly with 5-7 strands that have different sizes and appear alternately on the shaft. The leaves are round or elongated in width or heart, the upper surface is green and the surface is pale green. The flowers are small, 0.5-1 cm long and clustered in panicles. The pods are green to brown when ripe and are elongated lanceolate, pointed at the base and tip. The pods have 1-4 seeds which are soft and brownish. Indian rosewood grows at elevations below 600 m,...