scholarly journals Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae)

2018 ◽  
Author(s):  
Louise Brousseau ◽  
Paul V. A. Fine ◽  
Erwin Dreyer ◽  
Giovanni G. Vendramin ◽  
Ivan Scotti
Keyword(s):  
De Novo ◽  
Spatial Scales ◽  
Regional Scale ◽  
Biotic Interactions ◽  
Plant Responses ◽  
High Coverage ◽  
Protein Coding ◽  
Ecological Diversification ◽  
A Genome ◽  
Landscape Scales

AbstractPlant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees - whose large and undisturbed populations often span a variety of environmental conditions and local habitats - are particularly good models to study this process. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a replicated sampling design, to evaluate microgeographic adaptation in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae). A high-coverage genomic resource of ∼250 Mb was assembled de novo and annotated, leading to 32,789 predicted genes. 97,062 bi-allelic SNPs were detected over 25,803 contigs, and a custom Bayesian model was implemented to uncover candidate genomic targets of divergent selection. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence suggesting microgeographic divergence in functional traits, the discovery of genomic targets of microgeographic adaptation in the Neotropics is consistent with the hypothesis that local adaptation is a key driver of ecological diversification, operating across multiple spatial scales, from large- (i.e. regional) to microgeographic- (i.e. landscape) scales.

scholarly journals The human gene damage index as a gene-level approach to prioritizing exome variants

2015 ◽  
Vol 112 (44) ◽  
pp. 13615-13620 ◽  
Author(s):  
Yuval Itan ◽  
Lei Shang ◽  
Bertrand Boisson ◽  
Etienne Patin ◽  
Alexandre Bolze ◽  
...  
Keyword(s):  
General Population ◽  
De Novo ◽  
Damage Index ◽  
Monogenic Disease ◽  
Sequence Length ◽  
De Novo Mutations ◽  
Protein Coding ◽  
A Genome ◽  
Gene Level ◽  
Gene Damage

The protein-coding exome of a patient with a monogenic disease contains about 20,000 variants, only one or two of which are disease causing. We found that 58% of rare variants in the protein-coding exome of the general population are located in only 2% of the genes. Prompted by this observation, we aimed to develop a gene-level approach for predicting whether a given human protein-coding gene is likely to harbor disease-causing mutations. To this end, we derived the gene damage index (GDI): a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population. We found that the GDI was correlated with selective evolutionary pressure, protein complexity, coding sequence length, and the number of paralogs. We compared GDI with the leading gene-level approaches, genic intolerance, and de novo excess, and demonstrated that GDI performed best for the detection of false positives (i.e., removing exome variants in genes irrelevant to disease), whereas genic intolerance and de novo excess performed better for the detection of true positives (i.e., assessing de novo mutations in genes likely to be disease causing). The GDI server, data, and software are freely available to noncommercial users from lab.rockefeller.edu/casanova/GDI.

scholarly journals Global associations between terrestrial producer and vertebrate consumer diversity

2008 ◽  
Vol 276 (1655) ◽  
pp. 269-278 ◽  
Author(s):  
Walter Jetz ◽  
Holger Kreft ◽  
Gerardo Ceballos ◽  
Jens Mutke
Keyword(s):  
Plant Diversity ◽  
Environmental Conditions ◽  
Spatial Scales ◽  
Regional Scale ◽  
Scale Up ◽  
Biotic Interactions ◽  
Positive Association ◽  
Global Test ◽  
Strong Positive Association ◽  
Functionally Diverse

In both ecology and conservation, often a strong positive association is assumed between the diversity of plants as primary producers and that of animals, specifically primary consumers. Such a relationship has been observed at small spatial scales, and a begetting of diversity by diversity is expected under various scenarios of co-evolution and co-adaptation. But positive producer–consumer richness relationships may also arise from similar associations with past opportunities for diversification or contemporary environmental conditions, or from emerging properties of plant diversity such as vegetation complexity or productivity. Here we assess whether the producer–consumer richness relationship generalizes from plot to regional scale and provide a first global test of its strength for vascular plants and endothermic vertebrates. We find strong positive richness associations, but only limited congruence of the most diverse regions. The richness of both primary and higher-level consumers increases with plant richness at similar strength and rate. Environmental conditions emerge as much stronger predictors of consumer richness, and after accounting for environmental differences little variation is explained by plant diversity. We conclude that biotic interactions and strong local associations between plants and consumers only relatively weakly scale up to broad geographical scales and to functionally diverse taxa, for which environmental constraints on richness dominate.

scholarly journals Progress in plant genome sequencing: research directions

2019 ◽  
Vol 23 (1) ◽  
pp. 38-48 ◽  
Author(s):  
M. K. Bragina ◽  
D. A. Afonnikov ◽  
E. A. Salina
Keyword(s):  
Genome Sequencing ◽  
Plant Traits ◽  
Plant Genome ◽  
Targeted Sequencing ◽  
Genome Sequences ◽  
Crop Species ◽  
High Coverage ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
A Genome

Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.

scholarly journals Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

2019 ◽  
Author(s):  
Haley Wight ◽  
Junhui Zhou ◽  
Muzi Li ◽  
Sridhar Hannenhalli ◽  
Stephen M. Mount ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Rubus Idaeus ◽  
Slow Process ◽  
Red Raspberry ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Protein Coding Genes ◽  
A Genome ◽  
Exceptional Value

AbstractThe red raspberry, Rubus idaeus, is widely distributed in all temperate regions of Europe, Asia, and North America and is a major commercial fruit valued for its taste, high antioxidant and vitamin content. However, Rubus breeding is a long and slow process hampered by limited genomic and molecular resources. Genomic resources such as a complete genome sequencing and transcriptome will be of exceptional value to improve research and breeding of this high value crop. Using a hybrid sequence assembly approach including data from both long and short sequence reads, we present the first assembly of the Rubus idaeus genome (Joan J. variety). The de novo assembled genome consists of 2,145 scaffolds with a genome completeness of 95.3% and an N50 score of 638 KB. Leveraging a linkage map, we anchored 80.1% of the genome onto seven chromosomes. Using over 1 billion paired-end RNAseq reads, we annotated 35,566 protein coding genes with a transcriptome completeness score of 97.2%. The Rubus idaeus genome provides an important new resource for researchers and breeders.

scholarly journals De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aysenur Soyturk ◽  
Fatima Sen ◽  
Ali Tevfik Uncu ◽  
Ibrahim Celik ◽  
Ayse Ozgur Uncu
Keyword(s):  
Ab Initio ◽  
De Novo ◽  
Draft Genome ◽  
Mirna Precursor ◽  
Machine Learning Algorithms ◽  
Genomic Research ◽  
Support Vector ◽  
Cydonia Oblonga ◽  
Protein Coding ◽  
A Genome

AbstractQuince (Cydonia oblonga Mill.) is the sole member of the genus Cydonia in the Rosacea family and closely related to the major pome fruits, apple (Malus domestica Borkh.) and pear (Pyrus communis L.). In the present work, whole genome shotgun paired-end sequencing was employed in order to assemble the first draft genome of quince. A genome assembly that spans 488.4 Mb of sequence corresponding to 71.2% of the estimated genome size (686 Mb) was produced in the study. Gene predictions via ab initio and homology-based sequence annotation strategies resulted in the identification of 25,428 and 30,684 unique putative protein coding genes, respectively. 97.4 and 95.6% of putative homologs of Arabidopsis and rice transcription factors were identified in the ab initio predicted genic sequences. Different machine learning algorithms were tested for classifying pre-miRNA (precursor microRNA) coding sequences, identifying Support Vector Machine (SVM) as the best performing classifier. SVM classification predicted 600 putative pre-miRNA coding loci. Repetitive DNA content of the assembly was also characterized. The first draft assembly of the quince genome produced in this work would constitute a foundation for functional genomic research in quince toward dissecting the genetic basis of important traits and performing genomics-assisted breeding.

scholarly journals De novo phased assembly of the Vitis riparia grape genome

2019 ◽  
Author(s):  
Nabil Girollet ◽  
Bernadette Rubio ◽  
Pierre-François Bert
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Protein Coding ◽  
Important Species ◽  
Vitis Riparia ◽  
Fruit Species ◽  
Long Reads ◽  
A Genome

AbstractGrapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.

scholarly journals Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri

2020 ◽  
Author(s):  
Kazuaki Yamaguchi ◽  
Yuichiro Hara ◽  
Kaori Tatsumi ◽  
Osamu Nishimura ◽  
Jeramiah J. Smith ◽  
...  
Keyword(s):  
Single Copy ◽  
Sequence Information ◽  
High Coverage ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Genome Wide ◽  
Mate Pair ◽  
A Genome ◽  
Gene Models ◽  
High Utility

AbstractThe group of hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and is one of the only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming at reconstructing a high-coverage coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of resulting gene models promises a high utility in various comparative analyses including phylogenomics and phylome exploration.

scholarly journals The sequence and de novo assembly of Oxygymnocypris stewartii genome

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Hai-Ping Liu ◽  
Shi-Jun Xiao ◽  
Nan Wu ◽  
Di Wang ◽  
Yan-Chao Liu ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
De Novo ◽  
The Tibetan Plateau ◽  
Sequencing Data ◽  
Protein Coding ◽  
Sequencing Platform ◽  
A Genome ◽  
Altitude Adaptation ◽  
Oxygymnocypris Stewartii ◽  
Local Ecology

Abstract Animal genomes in the Qinghai-Tibetan Plateau provide valuable resources for scientists to understand the molecular mechanism of environmental adaptation. Tibetan fish species play essential roles in the local ecology; however, the genomic information for native fishes was still insufficient. Oxygymnocypris stewartii, belonging to Oxygymnocypris genus, Schizothoracinae subfamily, is a native fish in the Tibetan plateau living within the elevation from roughly 3,000 m to 4,200 m. In this report, PacBio and Illumina sequencing platform were used to generate ~385.3 Gb genomic sequencing data. A genome of about 1,849.2 Mb was obtained with a contig N50 length of 257.1 kb. More than 44.5% of the genome were identified as repetitive elements, and 46,400 protein-coding genes were annotated in the genome. The assembled genome can be used as a reference for future population genetic studies of O. stewartii and will improve our understanding of high altitude adaptation of fishes in the Qinghai-Tibetan Plateau.

scholarly journals Small to large-scale patterns of ground-dwelling spider (Araneae) diversity across northern Canada

FACETS ◽  
2018 ◽  
Vol 3 (1) ◽  
pp. 880-895 ◽  
Author(s):  
Sarah Loboda ◽  
Christopher M. Buddle
Keyword(s):  
Large Scale ◽  
Sampling Design ◽  
Spatial Scales ◽  
Regional Scale ◽  
Biotic Interactions ◽  
Longitudinal Patterns ◽  
Northern Canada ◽  
Multiple Spatial Scales ◽  
Spatial Influence ◽  
Total Species

We examined how Arctic spider (Araneae) biodiversity is distributed at multiple spatial scales in northern Canada using a standardized hierarchical sampling design. We investigated which drivers, environmental or spatial, influence the patterns observed. Spatial patterns of Arctic spider species richness and composition were assessed in 12 sites located in arctic, subarctic, and north boreal ecoclimatic regions, spanning 30 degrees of latitude and 80 degrees of longitude. Variation in diversity was partitioned in relation to multiple environmental and spatial drivers of diversity patterns. Over 23 000 adult spiders, representing 306 species in 14 families, were collected in northern Canada, with 107 species (35% of the total species collected) representing new territorial or provincial records. Spider diversity was structured at the regional scale across ecoclimatic regions but was not structured with latitude. Longitudinal patterns of spider diversity across Canada may be explained by post-glacial dispersal. At local scales, diversity was non-randomly distributed and possibly limited by biotic interactions. We recommend the use of ecoclimatic regions as a framework for conservation of biodiversity in northern Canada and spiders as useful bioindicators that can help us understand the effects of climate change across ecoclimatic regions of northern Canada.

scholarly journals Genome Update of Botrytis cinerea Strains B05.10 and T4

2012 ◽  
Vol 11 (11) ◽  
pp. 1413-1414 ◽  
Author(s):  
Martijn Staats ◽  
Jan A. L. van Kan
Keyword(s):  
Botrytis Cinerea ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Rna Seq ◽  
High Coverage ◽  
Protein Coding ◽  
Content Type ◽  
Gene Predictor ◽  
Structure Annotation ◽  
Expressed Sequence

ABSTRACT We report here an update of the Botrytis cinerea strains B05.10 and T4 genomes, as well as an automated preliminary gene structure annotation. High-coverage de novo assemblies and reference-based alignments led to a correction of wrong base calls, elimination of sequence gaps, and improved joining of contigs. The new assemblies have substantially lower numbers of scaffolds and a concomitant increase in the N 50 .The list of protein-coding genes was generated using the evidence-driven gene predictor Augustus, with expressed sequence tag evidence and RNA-Seq data as input.

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