scholarly journals Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing

2019 ◽  
Author(s):  
Miaomiao Lin ◽  
Jinbao Fang ◽  
Chungen Hu ◽  
Xiujuan Qi ◽  
Shihang Sun ◽  
...  
Keyword(s):  
Cold Resistance ◽  
Genomic Variation ◽  
Dna Polymorphisms ◽  
Future Research ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Sucrose Transport ◽  
Actinidia Arguta ◽  
Genome Wide ◽  
Insight Into

AbstractAmong the genus Actinidia, Actinidia arguta possesses the strongest cold resistance and produces fresh fruit with an intense flavor. To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating from different regions in China and identified the polymorphisms using InDel markers. In total, 4,710,650, 4,787,750, 4,646,026, and 4,590,616 SNPs and 1,481,002, 1,534,198, 1,471,304, and 1,425,393 InDels were detected in the ‘Ruby-3’, ‘Yongfeng male’, ‘Kuilv male’, and ‘Hongbei male’ genomes, respectively, compared with the reference genome sequence of ‘Hongyang’. A subset of 120 InDels were selected for re-sequencing validation. Additionally, genes related to non-synonymous SNPs and InDels in coding domain sequences were screened for functional analysis. The analysis of GO and KEGG showed that genes involved in cellular responses to water deprivation, sucrose transport, decreased oxygen levels and plant hormone signal transduction were significantly enriched in A. arguta. The results of this study provide insight into the genomic variation of kiwifruit and can inform future research on molecular breeding to improve cold resistance in kiwifruit.

scholarly journals Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. e0219884
Author(s):  
Miaomiao Lin ◽  
Jinbao Fang ◽  
Chungen Hu ◽  
Xiujuan Qi ◽  
Shihang Sun ◽  
...  
Keyword(s):  
Dna Polymorphisms ◽  
Whole Genome ◽  
Actinidia Arguta ◽  
Genome Wide

scholarly journals Genome-Wide Systematic Characterization of the NPF Family Genes and Their Transcriptional Responses to Multiple Nutrient Stresses in Allotetraploid Rapeseed

2020 ◽  
Vol 21 (17) ◽  
pp. 5947 ◽  
Author(s):  
Hao Zhang ◽  
Shuang Li ◽  
Mengyao Shi ◽  
Sheliang Wang ◽  
Lei Shi ◽  
...  
Keyword(s):  
N Uptake ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Peptide Transporter ◽  
Future Research ◽  
Whole Genome ◽  
Transcriptional Responses ◽  
Ammonium Toxicity ◽  
Genome Wide

NITRATE TRANSPORTER 1 (NRT1)/PEPTIDE TRANSPORTER (PTR) family (NPF) proteins can transport various substrates, and play crucial roles in governing plant nitrogen (N) uptake and distribution. However, little is known about the NPF genes in Brassica napus. Here, a comprehensive genome-wide systematic characterization of the NPF family led to the identification of 193 NPF genes in the whole genome of B. napus. The BnaNPF family exhibited high levels of genetic diversity among sub-families but this was conserved within each subfamily. Whole-genome duplication and segmental duplication played a major role in BnaNPF evolution. The expression analysis indicated that a broad range of expression patterns for individual gene occurred in response to multiple nutrient stresses, including N, phosphorus (P) and potassium (K) deficiencies, as well as ammonium toxicity. Furthermore, 10 core BnaNPF genes in response to N stress were identified. These genes contained 6–13 transmembrane domains, located in plasma membrane, that respond discrepantly to N deficiency in different tissues. Robust cis-regulatory elements were identified within the promoter regions of the core genes. Taken together, our results suggest that BnaNPFs are versatile transporters that might evolve new functions in B. napus. Our findings benefit future research on this gene family.

scholarly journals Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Prasanta K. Subudhi ◽  
Rama Shankar ◽  
Mukesh Jain
Keyword(s):  
Salt Tolerance ◽  
Dna Polymorphisms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Rice Varieties ◽  
Genome Wide ◽  
Rice Genotypes ◽  
Genome Level

AbstractSalinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing

2012 ◽  
Vol 10 (6) ◽  
pp. 623-634 ◽  
Author(s):  
Gopala K. Subbaiyan ◽  
Daniel L. E. Waters ◽  
Sanjay K. Katiyar ◽  
Ajanahalli R. Sadananda ◽  
Satyadev Vaddadi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dna Polymorphisms ◽  
Whole Genome ◽  
Genome Wide

scholarly journals Identification of a Goat Intersexuality-Associated Novel Variant Through Genome-Wide Resequencing and Hi-C

2021 ◽  
Vol 11 ◽  
Author(s):  
Guang-Xin E ◽  
Dong-Ke Zhou ◽  
Zhu-Qing Zheng ◽  
Bai-Gao Yang ◽  
Xiang-Long Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Genetic ◽  
Genetic Mechanism ◽  
Chromosome 1 ◽  
Future Research ◽  
Whole Genome ◽  
Chromosome Conformation ◽  
Next Generation Sequencing Technology ◽  
Genome Wide ◽  
Novel Variant

Background: Polled intersex syndrome (PIS) leads to reproductive disorders in goats and exerts a heavy influence on goat breeding. Since 2001, the core variant of an 11.7 kb deletion at ~129 Mb on chromosome 1 (CHI1) has been widely used as a genetic diagnostic criterion. In 2020, a ~0.48 Mb insertion within the PIS deletion was identified by sequencing in XX intersex goats. However, the suitability of this variation for the diagnosis of intersex goats worldwide and its further molecular genetic mechanism need to be clarified.Results: The whole-genome selective sweep of intersex goats from China was performed with whole-genome next-generation sequencing technology for large sample populations and a case–control study on interbreeds. A series of candidate genes related to the goat intersexuality phenotype were found. We further confirmed that a ~0.48 Mb duplicated fragment (including ERG and KCNJ15) downstream of the ~20 Mb PIS region was reversely inserted into the PIS locus in intersex Chinese goats and was consistent with that in European Saanen and Valais black-necked goats. High-throughput chromosome conformation capture (Hi-C) technology was then used to compare the 3D structures of the PIS variant neighborhood in CHI1 between intersex and non-intersex goats. A newly found structure was validated as an intrachromosomal rearrangement. This inserted duplication changed the original spatial structure of goat CHI1 and caused the appearance of several specific loop structures in the adjacent ~20 kb downstream region of FOXL2.Conclusions: Results suggested that the novel complex PIS variant genome was sufficient as a broad-spectrum clinical diagnostic marker of XX intersexuality in goats from Europe and China. A series of private dense loop structures caused by segment insertion into the PIS deletion might affect the expression of FOXL2 or other neighboring novel candidate genes. However, these structures require further in-depth molecular biological experimental verification. In general, this study provided new insights for future research on the molecular genetic mechanism underlying female-to-male sex reversal in goats.

scholarly journals Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing

2011 ◽  
Vol 52 (2) ◽  
pp. 274-282 ◽  
Author(s):  
Yuko Arai-Kichise ◽  
Yuh Shiwa ◽  
Hideki Nagasaki ◽  
Kaworu Ebana ◽  
Hirofumi Yoshikawa ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dna Polymorphisms ◽  
Japonica Rice ◽  
Whole Genome ◽  
Genome Wide

scholarly journals Loose ends in cancer genome structure

2021 ◽  
Author(s):  
Julie M Behr ◽  
Xiaotong Yao ◽  
Kevin Hadi ◽  
Huasong Tian ◽  
Aditya Deshpande ◽  
...  
Keyword(s):  
Large Scale ◽  
Structural Variation ◽  
Genome Structure ◽  
Cancer Genome ◽  
Genomic Variation ◽  
Future Research ◽  
Whole Genome ◽  
Structural Genomic ◽  
Short Read ◽  
Pan Cancer

Recent pan-cancer studies have delineated patterns of structural genomic variation across thousands of tumor whole genome sequences. It is not known to what extent the shortcomings of short read (≤ 150 bp) whole genome sequencing (WGS) used for structural variant analysis has limited our understanding of cancer genome structure. To formally address this, we introduce the concept of "loose ends" - copy number alterations that cannot be mapped to a rearrangement by WGS but can be indirectly detected through the analysis of junction-balanced genome graphs. Analyzing 2,319 pan-cancer WGS cases across 31 tumor types, we found loose ends were enriched in reference repeats and fusions of the mappable genome to repetitive or foreign sequences. Among these we found genomic footprints of neotelomeres, which were surprisingly enriched in cancers with low telomerase expression and alternate lengthening of telomeres phenotype. Our results also provide a rigorous upper bound on the role of non-allelic homologous recombination (NAHR) in large-scale cancer structural variation, while nominating INO80, FANCA, and ARID1A as positive modulators of somatic NAHR. Taken together, we estimate that short read WGS maps >97% of all large-scale (>10 kbp) cancer structural variation; the rest represent loose ends that require long molecule profiling to unambiguously resolve. Our results have broad relevance for future research and clinical applications of short read WGS and delineate precise directions where long molecule studies might provide transformative insight into cancer genome structure.

scholarly journals Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1407 ◽  
Author(s):  
Andy G. Lynch
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Data Set ◽  
Tumour Sample ◽  
Copy Numbers ◽  
Genome Wide ◽  
Insight Into ◽  
Shiny Application

It is now commonplace to investigate tumour samples using whole-genome sequencing, and some commonly performed tasks are the estimation of cellularity (or sample purity), the genome-wide profiling of copy numbers, and the assessment of sub-clonal behaviours. Several tools are available to undertake these tasks, but often give conflicting results – not least because there is often genuine uncertainty due to a lack of model identifiability. Presented here is a tool, "Crambled", that allows for an intuitive visual comparison of the conflicting solutions. Crambled is implemented as a Shiny application within R, and is accompanied by example images from two use cases (one tumour sample with matched normal sequencing, and one standalone cell line example) as well as functions to generate the necessary images from any sequencing data set. Through the use of Crambled, a user may gain insight into why each tool has offered its given solution and combined with a knowledge of the disease being studied can choose between the competing solutions in an informed manner.

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