Lara Pereira

Lara Pereira
The University of Sheffield | Sheffield · Department of Animal and Plant Sciences

About

30
Publications
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1,141
Citations

Publications

Publications (30)
Article
Full-text available
C4 photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4 is complicated by the fact that variation in photosynthetic type is usually segregated between species that diverged a long time ago....
Preprint
Full-text available
C4 photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4 is complicated by the fact that variation in photosynthetic type is usually segregated between species. Here, we perform a genome wid...
Article
Full-text available
Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We ident...
Article
Background: Numerous groups of plants have adapted to CO2 limitations by independently evolving C4 photosynthesis. This trait relies on concerted changes in anatomy and biochemistry to concentrate CO2 within the leaf and thereby boost productivity in tropical conditions. The ecological and economical importance of C4 photosynthesis has motivated i...
Article
C4 photosynthesis results from anatomical and biochemical characteristics that together concentrate CO2 around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), increasing productivity in warm conditions. This complex trait evolved through the gradual accumulation of components, and particular species possess only some of these, resulting...
Article
Full-text available
Methyl salicylate is an important inter- and intra-plant signaling molecule, but is deemed undesirable by humans when it accumulates to high levels in ripe fruits. Balancing the tradeoff between consumer satisfaction and overall plant health is challenging as the mechanisms regulating volatile levels have not yet been fully elucidated. In this stud...
Article
Full-text available
Societal Impact Statement Lateral gene transfer (LGT) refers to the transmission of genetic material without sexual reproduction. LGT is widespread in a number of plant species, including grasses. But how these genes of foreign origin got there is presently unknown. In this review, we show that transformation techniques used to genetically modify o...
Article
Full-text available
Melon is an economically important crop with widely diverse fruit morphology and ripening characteristics. Its diploid sequenced genome and multiple genomic tools make this species suitable to study the genetic architecture of fruit traits. With the development of this introgression line population of the elite varieties ‘Piel de Sapo’ and ‘Védrant...
Article
Methyl salicylate imparts a potent flavor and aroma described as medicinal and wintergreen that is undesirable in tomato(Solanum lycopersicum) fruit. Plants control the quantities of methyl salicylate through a variety of biosynthetic pathways, including the methylation of salicylic acid to form methyl salicylate and subsequent glycosylation to pre...
Preprint
Full-text available
Lateral gene transfer (LGT) has been reported in multiple eukaryotes. This process seems particularly widespread in the grass family, although we know very little about the underlying dynamics and how it impacts gene content variation within a species. Alloteropsis semialata is a tropical grass, and multiple LGT were detected in a reference genome...
Article
Full-text available
Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenoty...
Article
Full-text available
Key Message Six novel fruit weight QTLs were identified in tomato using multiple bi-parental populations developed from ancestral accessions. Beneficial alleles at these loci arose in semi-domesticated subpopulations and were likely left behind. This study paves the way to introgress these alleles into breeding programs. Abstract The size and weig...
Article
Full-text available
Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5, AL...
Article
Full-text available
Introgression lines are valuable germplasm for scientists and breeders, since they ease genetic studies such as QTL interactions and positional cloning as well as the introduction of favorable alleles into elite varieties. We developed a novel introgression line collection in melon using two commercial European varieties with different ripening beh...
Article
Aroma is an essential trait in melon fruit quality, but its complexity and genetic basis is still poorly understood. The aim of this study was the identification of quantitative trait loci (QTLs) underlying volatile organic compounds (VOCs) biosynthesis in melon rind and flesh, using a Recombinant Inbred Line (RIL) population from the cross ‘Piel d...
Article
When germinating in the light, Arabidopsis (Arabidopsis thaliana) seedlings undergo photomorphogenic development, characterized by short hypocotyls, greening, and expanded cotyledons. Stressed chloroplasts emit retrograde signals to the nucleus that induce developmental responses and repress photomorphogenesis. The nuclear targets of these retrogra...
Article
Full-text available
Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species, allowing the study of the processes that regulate this complex trait with genetic approaches. We phenotyped a population of recombinant inbred lines (RILs), obtained by crossing a climacteric (Vé...
Preprint
When germinating in the light, Arabidopsis seedlings undergo photomorphogenic development, characterized by short hypocotyls, greening and expanded cotyledons. Stressed chloroplasts emit retrograde signals to the nucleus that induce developmental responses and repress photomorphogenesis. The nuclear targets of these retrograde signals are not yet f...
Article
Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-sca...
Article
Full-text available
Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the s...
Article
Full-text available
Background Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. Results In order to identify QTLs co...
Conference Paper
Full-text available
Diversity in berry size and shape has been selected during grapevine domestication. While spherical shapes are more frequent in wine grapes to increase the proportion of secondary metabolites accumulated in the berry skin, larger berries with striking forms are attractive for table grape consumers. To gain insight on the molecular mechanisms genera...
Article
Ethylene is a gaseous plant hormone involved in defense, adaptations to environmental stress, and fruit ripening. Its relevance to the latter makes its detection highly useful to physiologists interested in ripening onset. Produced as a sharp peak during the respiratory burst, ethylene is biologically active at tens of nL?L(-1) . Reliable quantific...

Questions

Questions (5)
Question
Hello,
I am optimizing a protocol to visualize pollen tube growth in several grass species. I am using ethanol-glacial acetic acid to fix the flowers and then plan to re-hydrate them using serial ethanol solutions (70%, 50%, 30%, water). Then I will clear the tissue using a 8M Sodium Hydroxide solution. I was wondering which steps are time-sensitive and which ones are not. I think I have to keep the flowers in ethanol-glacial acetic acid for a certain amount of time (I am trying several concentration-duration combinations). I believe I can leave the samples in 70% ethanol for weeks without problem, but not in the Sodium Hydroxide solution. So after the clearing, if I want to storage the flowers for some time, what solution should I use? I am using aniline blue staining, would it be good to keep it in the staining solution for ~1-2 weeks?
Thank you in advance for your help.
Question
I am trying to calculate outcrossing rates in grasses. Most of the papers I found used a software called "MLTR" (https://www.nature.com/articles/6800029). The problem is that the link to download the paper does not seem to be working, and I tried to find an alternative way to find it but without any success. Does anyone know how to find the program and some tutorial/manual? Thank you in advance for your help.
Question
I am working with a few known genes in tomato. Although these genes have been cloned - so cDNA has been sequenced and experimental evidence proves its existence - they are not correctly annotated or even annotated at all in the most recent version of tomato genome. This fact complicates some downstream analysis, as RNAseq analysis or variant annotation. Is it possible to add a gene to a GFF file manually? Could I include it somehow in the databases I am working with? Thanks in advance for your help!
Question
I am studying the genetic diversity present in a collection of accessions for a few specific genes. I have VCF files as input data, and I am trying to use the R package 'pegas'. It seems really useful and straightforward, but the only issue I am having is because I am starting with VCF files instead of FASTA files. Do you have any advice? Is there any other package in R which would allow to work with VCF easily? Would it be best to generate first the sequences for each individual in FASTA format before starting the phylogenetic analysis?
Any suggestion is welcome. Thank you.
Question
I am currently working on tomato fruit quality, doing QTL mapping and fine mapping of genes involved in volatile pathways. The volatile quantification is generally performed by our collaborator, using a GC-FID instrument. Now I am considering to implement the quantification in my department, but using HS-SPME-GC-MS. I am mainly interested in relative values, for each experiment I will be comparing two groups (two genotypes) and I need to be confident enough about whether they are different or not. Do you think that SPME and GC-MS are accurate enough to do so? Thanks in advance.

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