scholarly journals Mastering the difficulties presented by the peculiarities of island life. A commentary on: ‘Reconstruction of the spatio-temporal diversification and ecological niche evolution ofHelianthemum(Cistaceae) in the Canary Islands using genotyping-by-sequence data’

2021 ◽  
Vol 127 (5) ◽  
pp. iii-iv
Author(s):  
Mark Carine
Keyword(s):  
Canary Islands ◽  
Ecological Niche ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Sequencing Data ◽  
Niche Evolution ◽  
Spatio Temporal

This article comments on:Rafael G. Albaladejo, Sara Martín-Hernanz, J. Alfredo Reyes-Betancort, Arnoldo Santos-Guerra, María Olangua-Corral and Abelardo Aparicio Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data, Annals of Botany, Volume 127, Issue 5, 16 April 2021, Pages 597–611, https://doi.org/10.1093/aob/mcaa090

scholarly journals Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data

2020 ◽  
Author(s):  
Rafael G Albaladejo ◽  
Sara Martín-Hernanz ◽  
J Alfredo Reyes-Betancort ◽  
Arnoldo Santos-Guerra ◽  
María Olangua-Corral ◽  
...  
Keyword(s):  
Canary Islands ◽  
Ecological Niche ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Genotyping By Sequencing ◽  
Niche Conservatism ◽  
Sequencing Data ◽  
History Of ◽  
Spatio Temporal ◽  
Dispersal Events

Abstract Background and Aims Several biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae). Methods We performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade. Key Results Our phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor. Conclusions The rapid and abundant diversification (0.75–1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.

Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with genotyping‐by‐sequencing data and niche modelling

2020 ◽  
Vol 47 (4) ◽  
pp. 993-1005 ◽  
Author(s):  
Irene Villa‐Machío ◽  
Alejandro G. Fernández de Castro ◽  
Javier Fuertes‐Aguilar ◽  
Gonzalo Nieto Feliner
Keyword(s):  
Canary Islands ◽  
Genotyping By Sequencing ◽  
Sequencing Data ◽  
Niche Modelling ◽  
Colonization History ◽  
History Of

scholarly journals Agro-morphological, yield, and genotyping-by-sequencing data of selected wheat germplasm

2020 ◽  
Author(s):  
Madiha Islam ◽  
Abdullah ◽  
Bibi Zubaida ◽  
Nosheen Shafqat ◽  
Rabia Masood ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Wheat Breeding ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Yield Data ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Short Reads

AbstractWheat (Triticum aestivum) is the most important staple food in Pakistan. Knowledge of its genetic diversity is critical for designing effective crop breeding programs. Here we report agro-morphological and yield data for 112 genotypes (including 7 duplicates) of wheat (Triticum aestivum) cultivars, advance lines, landraces and wild relatives, collected from several research institutes and breeders across Pakistan. We also report genotyping-by-sequencing (GBS) data for a selected sub-set of 52 genotypes. Sequencing was performed using Illumina HiSeq 2500 platform using the PE150 run. Data generated per sample ranged from 1.01 to 2.5 Gb; 90% of the short reads exhibited quality scores above 99.9%. TGACv1 wheat genome was used as a reference to map short reads from individual genotypes and to filter single nucleotide polymorphic loci (SNPs). On average, 364,074±54479 SNPs per genotype were recorded. The sequencing data has been submitted to the SRA database of NCBI (accession number SRP179096). The agro-morphological and yield data, along with the sequence data and SNPs will be invaluable resources for wheat breeding programs in future.

scholarly journals Application of genotyping-by-sequencing data on inferring the phylogeny of Curcuma (Zingiberaceae) from China

2019 ◽  
Author(s):  
Heng Liang ◽  
Yan Zhang ◽  
Jiabing Deng ◽  
Gang Gao ◽  
Chunbang Ding ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Reference Genome ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Morphological Differentiation ◽  
Genotyping By Sequencing ◽  
Tibet Plateau ◽  
Sequencing Data

Abstract Background: Genotyping-by-sequencing (GBS), as one of the next generation sequences, has been applied to large scale genotyping in plants, which is poor in morphological differentiation and low in genetic divergence among different species. Curcuma is a significantly medicinal and edible genus. Improvement efforts of phylogenetic relationships and disentangling species are still a challenge due to poor morphology and lack in a reference genome. Result: A high-throughput genomic sequence data which was obtained through GBS protocols was used to investigate the relationships among 8 species with 60 total samples of Curcuma. Through the use of the ipyrad software, 437,061 loci and 997,988 filtered SNPs without reliance upon a reference genome were produced. After quality control (QC) of the filtered SNPs, 1,295 high-quality SNPs were used to clarify the phylogenetic relationships among Curcuma species. Based on these data, a supermatrix approach was used to speculate the phylogeny, and the phylogenetic trees and the relationships were inferred . Conclusions: Varying degrees of support can be explained, as well as the diversification events for Chinese Curcuma. The diversification events showed that the third intense uplift of Qinghai–Tibet Plateau (QTP) and formation of the Hengduan Mountains may speed up Curcuma interspecific divergence in China. The PCA suggested the same topology of the phylogenetic tree. The genetic structure analysis revealed that extensive hybridization may exist in Chinese Curcuma. Additionally, the GBS will be a promising approach for the phylogenetic and systematic study in the future.

scholarly journals Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outcrossed mapping populations

2017 ◽  
Author(s):  
Chenxi Zhou ◽  
Bode Olukolu ◽  
Dorcus C. Gemenet ◽  
Shan Wu ◽  
Wolfgang Gruneberg ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Whole Genome Sequence ◽  
Sequencing Data ◽  
Ipomoea Trifida ◽  
High Coverage ◽  
Potato Genome ◽  
Plant Genomes ◽  
Mapping Populations

ABSTRACTThe assembly of whole-chromosome pseudomolecules for plant genomes remains challenging due to polyploidy and high repeat content. We developed an approach for constructing complete pseudomolecules for polyploid species using genotyping-by-sequencing data from outcrossing mapping populations coupled with high coverage whole genome sequence data of a reference genome. Our approach combines de novo assembly with linkage mapping to arrange scaffolds into pseudomolecules. We show that the method is able to reconstruct simulated chromosomes for both diploid and tetraploid genomes. Comparisons to three existing genetic mapping tools show that our method outperforms the other methods in accuracy on both grouping and ordering, and is robust to the presence of substantial amounts of missing data and genotyping errors. We applied our method to three real datasets including a diploid Ipomoea trifida and two tetraploid potato mapping populations. The linkage maps show significant concordance with the reference chromosomes. We resolved seven assembly errors for the published Ipomoea trifida genome assembly as well as anchored an unplaced scaffold in the published potato genome.

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

scholarly journals REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data

2020 ◽  
Author(s):  
Russell Lewis McLaughlin
Keyword(s):  
Structural Variation ◽  
Sequence Data ◽  
Neurological Diseases ◽  
Repeat Expansion ◽  
Sequencing Data ◽  
Short Read ◽  
Short Read Sequencing ◽  
Repeat Expansions ◽  
Paired End Sequencing

Abstract Motivation Repeat expansions are an important class of genetic variation in neurological diseases. However, the identification of novel repeat expansions using conventional sequencing methods is a challenge due to their typical lengths relative to short sequence reads and difficulty in producing accurate and unique alignments for repetitive sequence. However, this latter property can be harnessed in paired-end sequencing data to infer the possible locations of repeat expansions and other structural variation. Results This article presents REscan, a command-line utility that infers repeat expansion loci from paired-end short read sequencing data by reporting the proportion of reads orientated towards a locus that do not have an adequately mapped mate. A high REscan statistic relative to a population of data suggests a repeat expansion locus for experimental follow-up. This approach is validated using genome sequence data for 259 cases of amyotrophic lateral sclerosis, of which 24 are positive for a large repeat expansion in C9orf72, showing that REscan statistics readily discriminate repeat expansion carriers from non-carriers. Availabilityand implementation C source code at https://github.com/rlmcl/rescan (GNU General Public Licence v3).

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

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