De novo assembly and characterization of transcriptomes of early-stage fruit from two genotypes of Annona squamosa L. with contrast in seed number

Abstract

BackgroundAnnona squamosa L., a popular fruit tree, is the most widely cultivated species of the genus Annona. The lack of transcriptomic and genomic information limits the scope of genome investigations in this important shrub. It bears aggregate fruits with numerous seeds. A few rare accessions with very few seeds have been reported for Annona. A massive pyrosequencing (Roche, 454 GS FLX+) of transcriptome from early stages of fruit development (0, 4, 8 and 12 days after pollination) was performed to produce expression datasets in two genotypes, Sitaphal and NMK-1, that show a contrast in the number of seeds set in fruits. The data reported here is the first source of genome-wide differential transcriptome sequence in two genotypes of A. squamosa, and identifies several candidate genes related to seed development.ResultsApproximately 1.9 million high-quality clean reads were obtained in the cDNA library from the developing fruits of both the genotypes, with an average length of about 568 bp. Quality-reads were assembled de novo into 2074 to 11004 contigs in the developing fruit samples at different stages of development. The contig sequence data of all the four stages of each genotype were combined into larger units resulting into 14921 (Sitaphal) and 14178 (NMK-1) unigenes, with a mean size of more than 1 Kb. Assembled unigenes were functionally annotated by querying against the protein sequences of five different public databases (NCBI non redundant, Prunus persica, Vitis vinifera, Fragaria vesca, and Amborella trichopoda), with an E-value cut-off of 10−5. A total of 4588 (Sitaphal) and 2502 (NMK-1) unigenes did not match any known protein in the NR database. These sequences could be genes specific to Annona sp. or belong to untranslated regions. Several of the unigenes representing pathways related to primary and secondary metabolism, and seed and fruit development expressed at a higher level in Sitaphal, the densely seeded cultivar in comparison to the poorly seeded NMK-1. A total of 2629 (Sitaphal) and 3445 (NMK-1) Simple Sequence Repeat (SSR) motifs were identified respectively in the two genotypes. These could be potential candidates for transcript based microsatellite analysis in A. squamosa.ConclusionThe present work provides early-stage fruit specific transcriptome sequence resource for A. squamosa. This repository will serve as a useful resource for investigating the molecular mechanisms of fruit development, and improvement of fruit related traits in A. squamosa and related species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1248-3) contains supplementary material, which is available to authorized users.

The transition from somatic to germline identity shows conserved and specialized features during angiosperm evolution

“…To identify the PIN1 sequence from A. cherimola , we examined a recent transcriptome study from the closely related Annona squamosa (Gupta et al ., ). This led to the identification of a single PIN1‐ like sequence from A. cherimola cDNA.…”

Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size

“…Developing fruits at 0, 6, and 14 DAA were harvested randomly from three healthy trees each, of the two genotypes. The samples were surface sterilized with absolute ethanol before harvesting, as described previously7. The harvested samples were immediately frozen in liquid nitrogen and stored at −80 °C until RNA extraction.…”

“…In horticultural crops, only in a few cases, transcriptome sequence analysis has been used for the prediction of genes related to fruit development- as in case of Annona squamosa, Musa accuminata , Prunusavium , Pyrusbrets chneideri etc78910. Comparative analysis of transcriptome in litchi has been used to speculate on the processes involved in the regulation of floral initiation by phytohormones, expression of flowering related genes11, genes related to shading stress12, fruit cracking13, reactive oxygen species (ROS) induced abortion of rudimentary leaves14, fruit abscission15, maturation, coloration16, abscission induced by carbohydrate stress17 and fruit ripening after cold storage18.…”

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

“…As a commercially important fruit tree, sugar apple orchards are wide spread and well adapted to the edaphoclimatic conditions of tropical and subtropical zones. Due to its medicinal and nutritional properties, sugar apple tree is well known, and widely planted throughout the tropics (Gupta et al, 2015; Liu et al, 2015). The axillary buds of sugar apple are cryptic, obscured by the base of the petiole, and released following leaf abscission.…”