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

Gupta Y, Pathak AK, Singh K, Mantri SS, Singh SP, Tuli R - BMC Genomics (2015)

Bottom Line: 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.A total of 4588 (Sitaphal) and 2502 (NMK-1) unigenes did not match any known protein in the NR database.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.

View Article: PubMed Central - PubMed

Affiliation: National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology (DBT), C-127, Industrial Area, Phase-8, -160071, Mohali, India. yogesh@nabi.res.in.

ABSTRACT

Background: Annona 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.

Results: Approximately 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.

Conclusion: The 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.

Show MeSH
Mature fruits of Sitaphal (a) and NMK-1 (b), showing densely seeded and nearly seedless ripened carpels (Scale 2 cm), respectively. Bar diagram shows the difference between the two genotypes in fruit seed number (c). The error bars indicate standard error in thirty mature fruits, harvested from three different plants (10 fruits from each plant) of each genotype.
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Fig1: Mature fruits of Sitaphal (a) and NMK-1 (b), showing densely seeded and nearly seedless ripened carpels (Scale 2 cm), respectively. Bar diagram shows the difference between the two genotypes in fruit seed number (c). The error bars indicate standard error in thirty mature fruits, harvested from three different plants (10 fruits from each plant) of each genotype.

Mentions: Two Annona genotypes with contrast in fruit seed number (Figure 1), Sitaphal and NMK-1, were used in this study. Sitaphal is a well known cultivar of A. squamosa [22]. NMK-1 was developed by selection for desirable characteristics from a population of Annona genotypes [21]. However, systematic information on the development of the cultivars is not available. Phylogenetic analysis, using two marker sequences (rbcl and LMCH10) in seventeen species of Annona, placed both the genotypes close to A. squamosa (Additional file 1: Figure S1). The two genotypes were collected from the field of Madhuban Nursery (17.68° N 75.92° E coordinates, at an elevation of 457 m), Solapur, Maharshtra, India, where these are clonally propagated.Figure 1


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

Gupta Y, Pathak AK, Singh K, Mantri SS, Singh SP, Tuli R - BMC Genomics (2015)

Mature fruits of Sitaphal (a) and NMK-1 (b), showing densely seeded and nearly seedless ripened carpels (Scale 2 cm), respectively. Bar diagram shows the difference between the two genotypes in fruit seed number (c). The error bars indicate standard error in thirty mature fruits, harvested from three different plants (10 fruits from each plant) of each genotype.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4336476&req=5

Fig1: Mature fruits of Sitaphal (a) and NMK-1 (b), showing densely seeded and nearly seedless ripened carpels (Scale 2 cm), respectively. Bar diagram shows the difference between the two genotypes in fruit seed number (c). The error bars indicate standard error in thirty mature fruits, harvested from three different plants (10 fruits from each plant) of each genotype.
Mentions: Two Annona genotypes with contrast in fruit seed number (Figure 1), Sitaphal and NMK-1, were used in this study. Sitaphal is a well known cultivar of A. squamosa [22]. NMK-1 was developed by selection for desirable characteristics from a population of Annona genotypes [21]. However, systematic information on the development of the cultivars is not available. Phylogenetic analysis, using two marker sequences (rbcl and LMCH10) in seventeen species of Annona, placed both the genotypes close to A. squamosa (Additional file 1: Figure S1). The two genotypes were collected from the field of Madhuban Nursery (17.68° N 75.92° E coordinates, at an elevation of 457 m), Solapur, Maharshtra, India, where these are clonally propagated.Figure 1

Bottom Line: 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.A total of 4588 (Sitaphal) and 2502 (NMK-1) unigenes did not match any known protein in the NR database.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.

View Article: PubMed Central - PubMed

Affiliation: National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology (DBT), C-127, Industrial Area, Phase-8, -160071, Mohali, India. yogesh@nabi.res.in.

ABSTRACT

Background: Annona 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.

Results: Approximately 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.

Conclusion: The 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.

Show MeSH