Biology subjects

Mariac, C.

Publications and source records attributed to Mariac, C..

8 recordsLinked to original sources

bioRxiv2024

Picturing plant biodiversity from airborne environmental DNA.

While eDNA approaches have gained interest over the past decades all types of organisms have not been addressed evenly. In particular terrestrial plants have been the subject of less attention. Here we address the possibility to represent plant biodiversity from airborne environmental DNA (eDNA) sampling and metabarcoding. We collected air using a biological air sampler in the Botanical Garden of Montpellier (France) and compared the list of revealed plant species to the botanical inventory of the Garden. Ninety-two plant species could be detected from three sampling points across the 4,6 ha of the Garden, after one hour sampling allowing to filter 9 m3 of air. We recorded the plants carrying flowers at the time of the experiment, which allowed us to estimate that plants flowering at the time of the sampling could be detected 10 times more easily than plants that were not, given the number of plants carrying flowers. However, flowering is far from being required as a vast majority of plants still was detected without flowering. We also show that not all species orders are detected with the same probability, tree species being better represented in the sample than herbal plants, given the number of trees present in the garden. Finally using diagnostic species, present only once in the garden, we estimate that the maximum sampling distance allowed by the biological air sampler is at least 110 m. Our study underlines that air sampling is a promising method for monitoring terrestrial plant biodiversity and highlights the parameters that should be adjusted to optimize the approach.

genetics↗

bioRxiv2023

Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations

1.Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus. Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes. Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40{degrees} to 78{degrees}N, a reference genome for Bathycoccus calidus, and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: while MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the large outlier chromosome (BOC), a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome (SOC), associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish Bathycoccus prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets. 2. Significance statementEukaryotic phytoplankton are key to ocean ecosystems, yet their intraspecific genomic diversity is poorly understood. We present 28 high-quality genomes and their annotations of the cosmopolitan microalga Bathycoccus, revealing whole genome structural variations, chromosomal haplotype diversity linked to mating and viral resistance, and offering a genomic framework that complements metagenomic data to establish this picoalga as a model for functional and ecological studies.

genomics↗

bioRxiv2023

Population dynamics of the cosmopolitan eukaryotic picophytoplankton Bathycoccusduring seasonal blooms in the bay of Banyuls sur Mer (North Western Mediterraneansea)

BackgroundAlthough metabarcoding and metagenomic approaches have generated large datasets on worldwide phytoplankton species diversity, the intraspecific genetic diversity underlying the genetic adaptation of marine phytoplankton to specific environmental niches remains largely unexplored. This is mainly due to the lack of biological resources and tools for monitoring the dynamics of this diversity in space and time. ResultsTo gain insight into population diversity, a novel method based on INDEL markers was developed on Bathycoccus prasinos (Mamiellophyceae), an abundant and cosmopolitan species with strong seasonal patterns. Long read sequencing was first used to characterise structural variants among the genomes of six B. prasinos strains sampled from geographically distinct regions in the world ocean. Markers derived from identified insertions/deletions were validated by PCR then used to genotype 55 B. prasinos strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer (Mediterranean Sea, France). This led to their classification into eight multi-loci genotypes and the sequencing of strains representative of local diversity, further improving the available genetic diversity of B. prasinos. Finally, selected markers were directly tracked on environmental DNA sampled during 3 successive blooms from 2018 to 2021, showcasing a fast and cost-effective approach to follow local population dynamics. ConclusionsThis method, which involves (i) pre-identifying the genetic diversity of B. prasinos in environmental samples by PCR, (ii) isolating cells from selected environmental samples and (iii) identifying genotypes representative of B. prasinos diversity for sequencing, can be used to comprehensively describe the diversity and population dynamics not only in B. prasinos but also potentially in other generalist phytoplankton species.

ecology↗

bioRxiv2023

A strongly improved assembly of the pearl millet reference genome using OxfordNanopore long reads and optical mapping

Pearl millet (Pennisetum glaucum (L.)) R. Br. syn. Cenchrus americanus (L.) Morrone) is an important crop in South Asia and sub-Saharan Africa which contributes to ensure food security. Its genome has an estimated size of 1.76 Gb and displays a high level of repetitiveness above 80%. A first assembly was previously obtained for the Tift 23D2B1-P1-P5 cultivar genotype using short-read sequencing technologies. This assembly is however incomplete and fragmented with around 200 Mb unplaced on chromosomes. We report here an improved quality assembly of the pearl millet Tift 23D2B1-P1-P5 cultivar genotype obtained with an approach combining Oxford Nanopore long reads and Bionano Genomics optical maps. This strategy allowed us to add around 200 Mb at the chromosome-level assembly. Moreover we strongly improved continuity in the order of the contigs and scaffolds wihtin the chromosomes, particularly in the centromeric regions. Notably, we added more than 100 Mb around the centromeric region on chromosome 7. This new assembly also displayed a higher gene completeness with a complete BUSO score of 98.4% using the Poales database. This more complete and higher quality assembly of the Tift 23D2B1-P1-P5 genotype now available to the community will help in the development of research on the role of structural variants, and more broadly in genomics studies and the breeding of pearl millet.

genomics↗

bioRxiv2022

FrangiPANe, a tool for creating a panreference using left behind reads

We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2kb span. We annotated in addition 3,252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.

plant biology↗

bioRxiv2022

Optimization of capture protocols across species targeting up to 32000 genes and their extension to pooled DNA

PremiseIn-solution based capture is becoming a method of choice for sequencing targeted sequence. Methods and resultsWe assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single hybridization and showed it was an efficient and cost-effective strategy. We also extended the use of capture to pools of 100 samples and proved the efficiency of the method to assess allele frequency. Using a set of various organisms with different genome sizes, we demonstrated a correlation between the percentage of on-target reads vs. the relative size of the targeted sequences. ConclusionAltogether, we proposed methods, strategies, cost-efficient protocols and statistics to better evaluate and more effectively use hybridization capture.

evolutionary biology↗

bioRxiv2020

Aquaporins are main contributors of root hydraulic conductivity in pearl millet

Pearl millet is a key cereal for food security in arid and semi-arid regions but its yield is increasingly threatened by water stress. Physiological mechanisms consisting in saving water or increasing water use efficiency can alleviate that stress. Aquaporins (AQP) are water channels contributing to plant hydraulic balance that are supposedly involved in these mechanisms by mediating root water transport. However, AQP remain largely uncharacterized in pearl millet. Here, we studied AQP function in root water transport in two pearl millet lines contrasting for water use efficiency (WUE). We observed that these lines were also contrasting for root hydraulic conductivity (Lpr) and AQP contribution to Lpr, the line with lower WUE showing significantly higher AQP contribution to Lpr. To investigate the AQP isoforms contributing to Lpr, we developed genomic approaches to first identify the entire AQP family in pearl millet and second study the plasma membrane intrinsic proteins (PIP) gene expression profile. We identified and annotated 33 AQP genes in pearl millet among which ten encoded PIP isoforms. PgPIP1-3 and PgPIP1-4 were significantly more expressed in the line showing lower WUE, higher Lpr and higher AQP contribution to Lpr. Overall, our study suggests that AQP from the PIP1 family are the main contributor of Lpr in pearl millet and are possibly associated to whole plant water use mechanisms. This study paves the way for further investigations on AQP functions in pearl millet hydraulics and adaptation to environmental stresses. The newly sequenced nucleotide sequences reported in this article have been submitted to GenBank under the submission number 2333840 (TPA grp467567). Assignment of GenBank accession number is in process.

plant biology↗

bioRxiv2020

Transferability, development of Single Sequence Repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

In Sub-Saharan Africa, the fan palm Borassus aethiopum Mart. is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity of this palm species as well as its spatial structuration in Benin, West Africa. During a first phase we implemented a microsatellite markers-based approach relying on the reported transferability of primers developed in other palm species and found that, in disagreement with previously published results, only 22.5% of the 80 markers tested enabled amplification of African fan palm DNA and polymorphism detection was insufficient. During a second phase, we therefore generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of potential microsatellite markers. Among these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity in nine B. aethiopum populations. Our results show that genetic diversity of Beninese fan palm populations is low, with an overall average expected heterozygosity (He) of 0.354. Moreover, the positive values of the fixation index (F) in populations from both the Central (Soudano-Guinean) and the Southern (Guinean) regions suggest limited gene flows. Our analysis show that sampled B. aethiopum populations are clustered into two groups, one spanning populations from both the Southern and most of the Central region, and the other including the Central population of Save (which also has the highest He) and populations from the North. In light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.

genetics↗