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From the Glory Bush tree to the Queen Palm

The size of the genome of 100 Brazilian trees varies by up to a factor of twenty

How about sequencing the genome of a Brazilian tree? The idea was good, even more so in a country that usually is pointed to as the world champion in biodiversity. There was only one problem: nobody knew what was the approximate size of all of the genetic material present in the chromosomes of a arboreal species. If it were to be very large, the genome of a tree would be an uninspiring factor to a whole sequencing project. This was the situation back in 2001, when the proposal was put forward and, through lack of information, did not go any further. Now the picture has changed – and how. The size of the genome of more than a hundred trees native to Brazil have just been determined by the agronomy engineer Marcelo Carnier Dornelas, one of the researchers who participated in those discussions some four years ago. The results of the work indicate that there is not a standard size for the genome of a tree. The number of pairs of DNA bases of one species can be up to twenty times greater than that of another. The genome is made up of the grouping of an organism’s genes and the molecular information that control the working of those genes.

With its typical red flowers that color towns and cities between Carnival and Easter, the Glory Bush tree (Thibouchina granulosa) has the smallest genome. It has 340 million nitrogen pairs of bases, the chemical units that make up its DNA. The largest is that of the Queen Palm (Syagrus romanzoffiana), a type of palm tree, also easily found in the urban environment, whose juicy and orange colored fruit serves as a meal for animals in non-urban areas. The genetic material of this plant exhibits 6.2 billion pairs of bases, double the quantity of the “chemical letters” found in human DNA. The study, which will shortly be published in the magazine Annals of Botany, also brought out the fact that there is no clear relationship between the size of a tree and its genome, the example of which had previously been demonstrated in animal species and in other types of vegetables. Found within the Atlantic Rainforest, the Glory Bush tree and the Queen Palm exhibit crowns of more or less equivalent height, around 10 meters, and the diameter of their trunks comes in at around 40 centimeters. In spite of such biological similarity, both of the trees show genetic material of a size that is highly distinctive. In order to give greater security to their work, Dornelas determined the size of the genomes present in the nucleus of the tree?s cells by way of two distinct methods, flow cytometry and microdensitometry of the image. Both these techniques were originally conceived for use in the diagnosis of cancer.

Chemical letters
One must not confuse the study of agronomy engineering, which measured the size of 118 species of trees, with the work of the sequencing of the genetic material of these plants, a task that is much more complex. These are two very different things. The researcher estimated how many “chemical letters” exist in the DNA of each species, but did not determine in what order these nitrogenous bases appear in each one of the genomes. The information produced will serve as a reference for eventual sequencing projects. The data has shown that trees show DNA of a smaller size, and indeed, they will be easier to be sequenced. This is not the case of the famous and today little abundant Pernambuco wood (Caesalpinia echinata), which exhibits an enormous DNA, with 3.8 billion pairs of bases. “If one day we wanted to sequence the complete genome of a tree, the Pernambuco Wood would not be one of those likely to be chosen”, says Dornelas, who finished his post doctorate study at the Agricultural Nuclear Energy Center (Cena) of the University of São Paulo, in the town of Piracicaba, and in July assumed the post of professor at the Vegetal Physiology Department of the Biology Institute of the Campinas State University (Unicamp). “Perhaps it’ll be the mahogany tree, who knows?” Of the trees with highly priced wood, the Swietenia macrophyla, the scientific name of the mahogany tree, is one of those that has a smaller genome. Its genetic material is made up of 513 million pairs of bases.

Up until now the genome of only one tree, the Populus trichocarpa, the black cottonwood, a type from the northern hemisphere and of major economic importance, has been totally sequenced. An international consortium completed this work during September of last year. The genetic material of this type of aspen is considerably greater than that of the mahogany tree and contains around 50,000 genes, a fifth of them probably typical of trees and not found in other types of vegetables, such as the Arabidopsis thaliana, a harmful temperate climate herb, a relative of mustard, which functions as a plant model for biological studies.

To confront the size of the genomes of distinct species helps to demystify the idea that living things with a larger quantity of DNA are always more complex than organisms endowed with genetic material of a reduced dimension. If this were to be the case, some amebas, which have hundreds of billions of pairs of bases in their genome, would be the most sophisticated form of life on earth. “To have a large genome is not synonymous with greater complexity of an organism”, explains the biologist Fernando Reinach, the president of the biotechnology company Alellyx and the executive director of the company Votorantim Novos Negócios. “It’s like finding that the complexity of a country has some relationship with its number of inhabitants.” In the same manner, it would be incorrect to think that the Queen Palm tree is more complex than the Glory Bush tree only because its DNA is twenty times larger.

Shrunk genome
In some groups of trees with common characteristics, the size of the genome seems to be more or less similar, although it would be risky to make generalizations starting from data of only a hundred species. The genome of four arboreal species of the Anacardiaceae family, whose trademark is to produce fruit in the shape of a heart, do not show major variations in size: the smallest, that of the Brazilian Pepper tree (Shinus molle), has some 410 million pares of bases; the largest, that of the Cashew tree (Anacardium occidentale), has 50% more of these “chemical letters”. In other cases, perhaps due to the greater number of species analyzed, the apparent discrepancies call the attention to a greater degree. Two species of the Annonaceae family exhibit genomes of distinctly different sizes: the genetic material of the Monkey Pepper tree (Xylopia aromatica) is five times greater than that of the Annona coriacea.

From the evolutionary point of view, there are some theses circulating in the academic circles concerning the possible significance of genome size. One of them is that the genetic material of angiosperm plants (those that produce flowers) with their origin more remote on the timescale would be smaller than the more recent vegetables belonging to the same group. If this were to make sense, the São Paulo researcher could well have found an exception to the rule between the Myrtoidae, a branch of the Myrtaceae family that makes up the trees with succulent fruit, such as the guava (Psidium guajava) and the Myrciaria cauliflora. Dornelas estimated the DNA size of twenty species of Myrtoidae and perceived that all of them were smaller than those of the plants from the sub-family Leptospermoideae, another branch of the Myrtaceae family, made up of trees that produce dry fruit, whose appearance in nature is considered to have taken place before their relatives that produce succulent fruit. “It seems that within the Myrtaceae family there was, during the evolutionary process, a shrinkage in the size of the genomes”, the researcher says.

Another interesting comparative piece of data: trees of the Tabebuia genre, popularly known as pau d’arco (ipês), with yellow flowers, tend to present a larger genome than those that give red or white flowers. At least this is what came out of the analysis of the genome size of ten species of this genre. The yellow pau d’arco show a DNA with more than 2 billion pairs of bases; the red have just more than 1 billion pairs of bases; and the white around 900 million pairs of bases. A possible explanation for this phenomenon would be the greater number of chromosomes in the yellow ones. These trees have two pairs of 40 chromosomes. 80 in total, double the number found in the red pau d’arcos and the white pau d’arco. By this line of reasoning, over a number of generations, the increase (or decrease) in the number of chromosomes would lead to alterations in the external traits of the various species known as the paus d’arcos, bringing about a change in color of their flowers.

Comparative studies
As can be noted, to know the genome size of an organism does not serve only to point towards eventual candidates in the queue for sequencing. It is also an important piece of data for future comparative studies in the area of botany. According to one piece of scientific research published in January of this year and carried out by the researchers Michael Bennett and Ilia Leitch, From Royal Botanic Gardens, Kew, in London, there is data concerning the genome size of around 4,100 plants of the angiosperm group, which included herbs, shrubs and trees that produce flowers. “With some exceptions, this sample is dominated by plants of commercial importance and their wild relatives, model species cultivated for experimental use, and other species that have been grown close to laboratories in temperate regions, above all in Western Europe and North America.”, wrote the pair of researchers in the article published in Annals of Botany. The study by agronomist Dornelas is the first registration on the size of genetic material of plants belonging to 60 genres and 9 families of trees. “It’s an important piece of work even more so because of it’s specific Brazilian focus”, commented Carlos Alberto Labate, from the Genetics Department of the Luiz de Queiroz Upper school of Agriculture (Esalq) of USP. “And it should attract the interest of other researchers in the areas of conservation and evolution.”

The Project
The genomic profile of Brazilian trees – genetic biodiversity:  a bridge between the Biota and the AEG (nº 02/12778-1); Modality Research Assistance; Coordinator Marcelo Carnier Dornelas –  Cena/USP; Investiment R$ 3,000.00 and US$ 32,033.00 (FAPESP)