In Silico Prediction of Cell Wall Remodeling Genes in Tomato, Banana, Melon and Grape

Year 2019, Volume: 2 Issue: 2, 108 - 121, 12.08.2019

Nurul Hidayah Samsulrizal , Nik Yusnoraini Yusof

https://doi.org/10.38001/ijlsb.571315

Cited By: 2

Abstract

Ripening
is a complex developmental process and involves many events such as textural
and constitutional changes. The texture of fleshy fruits is one of the major
criteria for consumer choice. However, the molecular determinants of ripening-
associated changes in texture or “softening” are relatively poorly understood
and seem to involve a large number of cell wall remodelling factors. The recent
completion of the tomato genome sequence has revealed more than 50 cell wall
structure-related genes that are expressed during fruit development and
ripening and may impact texture changes in this fruit. The aim of the project
is to compare, on a genome-wide scale, ripening-related gene expression in a
range of fleshy fruits and especially those linked with cell wall remodelling.
Then by identifying orthologous genes in different fruit species to make
predictions about those genes likely to important for the softening process in
all fleshy fruits. Comparative genomics analysis of tomato (Solanum lycopersicum), banana (Musa acuminate), melon (Cucumis melo) and grape (Vitis vinifera), has been undertaken
using Inparanoid, Multiparanoid and BLAST2GO software. This analysis showed
that a total of 8,982 (25.86%) gene models could be identified in common
between all four genomes based on comparison of amino acid sequences. Of these
genes, 262 in tomato, 252 in grape, 261 in melon, and 198 in banana were
identified as encoding cell wall structure-related proteins. However,
comparison of the expression patterns of these genes revealed that most were
expressed in tissues other than ripening fruits, and of the fruit expressed
genes only a small number were common between different fruit species. This in silico analysis should provide
additional clues as a target for manipulation of fruit softening in a range of
fleshy fruit species. These also provide new opportunities to develop varieties
of tomatoes that can survive the trip from the farm to the grocery store whilst
maintaining excellent flavour and shelf-life.

Keywords

comparative genomics, inparanoid, cell wall

Supporting Institution

International Islamic University Malaysia (IIUM)

Project Number

RIGS17-022-0597

Thanks

I wish to thank International Islamic University Malaysia (IIUM) Research Initiative Grant Scheme (RIGS17-022-0597) for sponsored this work and The University of Nottingham UK for providing the facilities and technical assistant.

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