The secret life of melons revealed: 'Jumping sequences' may alter gene expression

Date:
August 25, 2020
Source:
University of Tsukuba
Summary:
Researchers find that retrotransposons (a.k.a. 'jumping sequences')
may affect gene expression in melons.



FULL STORY ==========================================================================
On the surface, the humble melon may just look like a tasty treat to
most. But researchers from Japan have found that this fruit has hidden
depths: retrotransposons (sometimes called "jumping sequences") may
change how genes are expressed.


==========================================================================
In a study published recently in Communications Biology, researchers
from the University of Tsukuba and the National Agriculture and Food
Research Organization (NARO) have revealed that retrotransposons had a
role in altering gene expression when melon genomes were diversifying,
and may affect gene expression that induces fruit ripening.

Melons comprise one of the most economically important fruit crops
globally. A special feature of melons is the coexistence of two fruit
types: climacteric (which produce ethylene and exhibit a burst in cellular respiration as ripening begins), and non-climacteric. Ethylene is a plant hormone important to the regulation of climacteric fruit-ripening traits
such as shelf life, which is of major economic importance.

"Because Harukei-3 melons produce ethylene during ripening, we wanted to
look at ethylene-related gene expression in this type of melon," says
lead author of the study Professor Hiroshi Ezura. "Harukei-3 produces
an especially sweet fruit if grown in the right seasons. Because of its
taste and attractive appearance, Harukei-3 has been used for a long
time in Japan as a standard type for breeding high-grade muskmelon."
To examine ethylene-related gene expression, the researchers assembled
the whole genome sequence of Harukei-3 by using third-generation nanopore sequencing paired with optical mapping and next-generation sequencing.

"We compared the genome of Harukei-3 with other melon
genomes. Interestingly, we found that there are genome-wide
presence/absence polymorphisms of retrotransposon-related sequences
between melon accessions, and 160 (39%) were transcriptionally induced
in post-harvest ripening fruit samples. They were also co-expressed
with neighboring genes," explains Dr. Ryoichi Yano, senior author. "We
also found that some retrotransposon-related sequences were transcribed
when the plants were subjected to heat stress." Retrotransposons are transposons (also referred to as "jumping sequences" because they can
change their positions within a genome) with sequences similar to those
of retroviruses.

"Our findings suggest that retrotransposons contributed to changes in gene expression patterns when melon genomes were diversifying. Retrotransposons
may also affect gene expression that brings on fruit ripening," says
Professor Ezura.

The Harukei-3 genome assembly, together with other data generated in this study, is available in the Melonet-DB database. Combined with future
updates, this database will contribute to the functional genomic study
of melons, especially reverse genetics using genome editing.


========================================================================== Story Source: Materials provided by University_of_Tsukuba. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Ryoichi Yano, Tohru Ariizumi, Satoko Nonaka, Yoichi Kawazu,
Silin Zhong,
Lukas Mueller, James J. Giovannoni, Jocelyn K. C. Rose, Hiroshi
Ezura.

Comparative genomics of muskmelon reveals a potential
role for retrotransposons in the modification of gene
expression. Communications Biology, 2020; 3 (1) DOI:
10.1038/s42003-020-01172-0 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200825110729.htm

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