Chromosome‐level de novo genome assembly and whole‐genome resequencing of threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

2021 ◽  
Author(s):  
Bo Xu ◽  
Min Liao ◽  
Heng‐ning Deng ◽  
Chao‐chao Yan ◽  
Lv Yun‐yun ◽  
...  
Keyword(s):  
Threatened Species ◽  
Genome Assembly ◽  
De Novo ◽  
Biodiversity Hotspot ◽  
Whole Genome ◽  
Alpine Plant ◽  
Genome Resequencing ◽  
De Novo Genome Assembly ◽  
Whole Genome Resequencing ◽  
Chromosome Level

scholarly journals The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Peng Zhao ◽  
Guiliang Xin ◽  
Feng Yan ◽  
Huan Wang ◽  
Xiaolong Ren ◽  
...  
Keyword(s):  
Breeding System ◽  
De Novo ◽  
Whole Genome ◽  
Genome Resequencing ◽  
De Novo Genome Assembly ◽  
Genome Scans ◽  
Breeding System Evolution ◽  
Whole Genome Resequencing ◽  
Key Aspects ◽  
Shed Light

AbstractTapiscia sinensis (Tapisciaceae) possesses an unusual androdioecious breeding system that has attracted considerable interest from evolutionary biologists. Key aspects of T. sinensis biology, including its biogeography, genomics, and sex-linked genes, are unknown. Here, we report the first de novo assembly of the genome of T. sinensis. The genome size was 410 Mb, with 22,251 predicted genes. Based on whole-genome resequencing of 55 trees from 10 locations, an analysis of population genetic structure indicated that T. sinensis has fragmented into five lineages, with low intrapopulation genetic diversity and little gene flow among populations. By comparing whole-genome scans of male versus hermaphroditic pools, we identified 303 candidate sex-linked genes, 79 of which (25.9%) were located on scaffold 25. A 24-kb region was absent in hermaphroditic individuals, and five genes in that region, TsF-box4, TsF-box10, TsF-box13, TsSUT1, and TsSUT4, showed expression differences between mature male and hermaphroditic flowers. The results of this study shed light on the breeding system evolution and conservation genetics of the Tapisciaceae.

scholarly journals Identification of genetic variations in Necator americanus through resequencing by whole genome amplification

2019 ◽  
Vol 47 (9) ◽  
pp. 4353-4364
Author(s):  
Yumei Liu ◽  
Hongxuan Liu ◽  
Yuefeng Xie ◽  
Baohuan Zhang ◽  
Xiaoqian Zou ◽  
...  
Keyword(s):  
De Novo ◽  
Multiple Displacement Amplification ◽  
Genetic Variations ◽  
Whole Genome ◽  
Genome Resequencing ◽  
De Novo Genome Assembly ◽  
Go Analysis ◽  
Necator Americanus ◽  
New Strategy ◽  
Whole Genome Resequencing

Objective To describe a new strategy for the whole genome resequencing of small parasite samples. Methods Whole genome resequencing was based on a multiple displacement amplification (MDA) method. Sequencing reads were aligned with the reference genome, and a Bayesian model was used to calculate genotype probabilities. De novo genome assembly was conducted, and single nucleotide polymorphisms (SNPs) were detected. Gene ontology (GO) analysis was used to determine connections between SNPs and genes. Results In total, 64.12% of the parasite genome sequence was mapped to Necator americanus. fa, and 125,553 SNPs were detected. GO analysis revealed that most SNPs in coding regions were probably associated with common drug targets. Conclusion These results reveal the feasibility of a new strategy to detect genetic variations of small parasites. This study also provides a proof-of-principle for the molecular classification and epidemiological analysis of other parasites.

Chromosome‐level de novo genome assembly of Sarcophaga peregrina provides insights into the evolutionary adaptation of flesh flies

2020 ◽  
Vol 21 (1) ◽  
pp. 251-262
Author(s):  
Lipin Ren ◽  
Yanjie Shang ◽  
Li Yang ◽  
Shiwen Wang ◽  
Xiang Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Evolutionary Adaptation ◽  
De Novo Genome Assembly ◽  
Flesh Flies ◽  
Chromosome Level

scholarly journals A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 144 ◽  
Author(s):  
Laís Coelho ◽  
Lukas Musher ◽  
Joel Cracraft
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
De Novo ◽  
Structural Difference ◽  
Whole Genome ◽  
Sequencing Technology ◽  
A Genome ◽  
Avian Genomes ◽  
Chromosome Level

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

scholarly journals Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2740
Author(s):  
Yuya Liang ◽  
Shichen Wang ◽  
Chersty L. Harper ◽  
Nithya K. Subramanian ◽  
Rodante E. Tabien ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Global Climate ◽  
Major Effect ◽  
Sequence Information ◽  
Whole Genome ◽  
Submergence Tolerance ◽  
De Novo Genome Assembly ◽  
Rice Varieties ◽  
Genome Profile

Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).

scholarly journals Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

2020 ◽  
Author(s):  
Alia Parveen ◽  
Christa D. Jackson ◽  
Shatovisha Dey ◽  
Katy Tarrant ◽  
Nicholas B Anthony ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Chicken Chromosome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Whole Genome Resequencing ◽  
Ascites Syndrome

Abstract Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

scholarly journals Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C

2022 ◽  
Author(s):  
Stephanie H. Chen ◽  
Maurizio Rossetto ◽  
Marlien Merwe ◽  
Patricia Lu‐Irving ◽  
Jia‐Yee S. Yap ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
New South ◽  
New South Wales ◽  
De Novo Genome Assembly ◽  
South Wales ◽  
Long Reads ◽  
Chromosome Level

scholarly journals Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

2020 ◽  
Author(s):  
Alia Parveen ◽  
Christa Jackson ◽  
Shatovisha Dey ◽  
Katy Tarrant ◽  
Nicholas B Anthony ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Chicken Chromosome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Whole Genome Resequencing ◽  
Ascites Syndrome

Abstract Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

Sign in / Sign up

Export Citation Format

Share Document