Nav: Home

A simple software error corrected: bittersweet chloroplast genome becomes the model

May 16, 2018

The first complete plastome nucleotide sequence was published in 1986 for tobacco (Nicotiana tabacum L.) of the nightshade family (Solanaceae). This economically important mega-diverse plant family contains well-known crops and ornamentals such as potato, tomato, eggplants and petunias. In the study published in PLoS ONE researchers of the Finnish Museum of Natural History (LUOMUS) of the University of Helsinki sequenced the plastid genome of bittersweet (Solanum dulcamara L.) to provide genomic resources for chloroplast engineering. It is a diploid weed commonly found also in Finland, and has resistance to most important potato disease late blight caused by a water mold (oomycete) Phytophthora infestans.

The research turned out to be more important than initially thought:

"When we tried to compare the bittersweet plastome to other nightshade species we realized it cannot be done properly since genome annotations seem to contain so many errors," says the leader of the research Péter Poczai.

The study showed for the first time that these errors are due to one simple outdated software used worldwide. As a consequence, these errors are copied and propagated from one sequence to another in genetic databases.

"With hard work and manual editing we have corrected these errors for all solanaceous genomes, which place the bittersweet as a model for nightshade chloroplast comparative genomics. The wake of the errors in annotation is alive in plastid genomics in general since most of the sequencing projects are using this outdated software, which we are convinced needs to be replaced with a more advanced tool already planned as our next cutting-edge project," Ali Amiryousefi, PhD student in LUOMUS and first author of the study adds.

A new hypothesis of the ancestral genome presented

Only after these improvements, the LUOMUS group was finally able to make the comparative analysis of all nightshade plastid genomes, where they present hypothesis of the ancestral genome. With this they were able to show that structural re-arrangements are coinciding with bigger evolutionary changes of this family. The plastid genome sequence of the common weed bittersweet will help in benchmarking nightshade plastid genome annotations and could be used as a reliable reference in further studies.

"The present study is part of our research using the living greenhouse and herbarium collections of LUOMUS for sequencing chloroplast genomes and investigating the diversity of flowering plants. So far, we have sequenced 30 plastid genomes from our collections and first results are now starting to be published" summarizes Poczai.
-end-


University of Helsinki

Related Natural History Articles:

Charting the skies of history
Ice cores and ancient sediments can be gleaned for clues to weather and climate in the past.
Tree scars record 700 years of natural and cultural fire history in a northern forest
Distinguishing human from climatic influence on historical fire patterns is critical to forest management planning, which is guided by historical patterns of fire frequency, size, and intensity.
Caves in central China show history of natural flood patterns
Researchers at the University of Minnesota have found that major flooding and large amounts of precipitation occur on 500-year cycles in central China.
Russia-China: History and culture
2017 is an anniversary year for all Russian sinologists. In the approaching 2017 Russian academic Oriental Studies will turn 200 years, and it will be 180 years since formation of first department of Chinese verbal folklore in Kazan Imperial University; 60 years since foundation of Russian-Chinese friendship Community and 10 years since foundation of Confucius Institute of Kazan (Volga Region) Federal University (CI KFU).
History of cells told through MEMOIR
A new technique called MEMOIR can record the life history of animal cells.
The mathematics of music history
New research from Center for Music in the Brain shows that patriotism in music is expressed through use of speech rhythms from the composer's native language.
The history of beer yeast
Today's industrial yeast strains are used to make beer, wine, bread, biofuels, and more, but their evolutionary history is not well studied.
More natural history training needed, survey shows
A survey of early-career scientists and environmental-science professionals found that only 11 percent felt their academic training alone provided the needed exposure to natural history, which can be defined as the observation of organisms in their natural environment.
Natural history museum professionals, biodiversity scientists identify needs
Today, the Biodiversity Collections Network released a report, 'Building a More Networked System for Communicating about Natural History Collections.' This report includes overarching recommendations for how the biodiversity sciences community can improve communication within the community and with key decision-makers.
Your viruses could reveal your travel history, and more
The genomes of two distinct strains of the virus that causes the common lip cold sore, herpes simplex virus type 1, have been identified within an individual person -- an achievement that could be useful to forensic scientists for tracing a person's history.

Related Natural History Reading:

Natural History: The Ultimate Visual Guide to Everything on Earth (Smithsonian)
by DK (Author)

The Art of Natural History: Botanical Illustrations, Ornithological Drawings, and Other Masterpieces from the Age of Exploration
by Pascale Heurtel (Author), Michelle Lenoir (Author)

Dinosaurs: A Concise Natural History
by David E. Fastovsky (Author), David B. Weishampel (Author), John Sibbick (Illustrator)

Trees: Their Natural History
by Peter A. Thomas (Author)

A Natural History of the Sonoran Desert
by Steven John Phillips (Editor), Patricia Wentworth Comus (Editor), Mark Alan Dimmitt (Editor), Linda M. Brewer (Editor)

The Feather Thief: Beauty, Obsession, and the Natural History Heist of the Century
by Kirk Wallace Johnson (Author)

Natural Histories: Extraordinary Rare Book Selections from the American Museum of Natural History Library
by American Museum of Natural History (Author), Tom Baione (Editor)

Curators: Behind the Scenes of Natural History Museums
by Lance Grande (Author)

A Natural History of California: Second Edition
by Allan A. Schoenherr (Author)

Worlds of Natural History
by Helen Anne Curry (Editor), Nicholas Jardine (Editor), James Andrew Secord (Editor), Emma C. Spary (Editor)

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Approaching With Kindness
We often forget to say the words "thank you." But can those two words change how you — and those around you — look at the world? This hour, TED speakers on the power of gratitude and appreciation. Guests include author AJ Jacobs, author and former baseball player Mike Robbins, Dr. Laura Trice, Professor of Management Christine Porath, and former Danish politician Özlem Cekic.
Now Playing: Science for the People

#509 Anisogamy: The Beginning of Male and Female
This week we discuss how the sperm and egg came to be, and how a difference of reproductive interest has led to sexual conflict in bed bugs. We'll be speaking with Dr. Geoff Parker, an evolutionary biologist credited with developing a theory to explain the evolution of two sexes, about anisogamy, sexual reproduction through the fusion of two different gametes: the egg and the sperm. Then we'll speak with Dr. Roberto Pereira, research scientist in urban entomology at the University of Florida, about traumatic insemination in bed bugs.