scholarly journals Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 843 ◽  
Author(s):  
Ran Zhou ◽  
David Macaya-Sanz ◽  
Jeremy Schmutz ◽  
Jerry W. Jenkins ◽  
Gerald A. Tuskan ◽  
...  
Keyword(s):  
Sex Determination ◽  
Populus Trichocarpa ◽  
Orthologous Gene ◽  
Inverted Repeats ◽  
Homologous Gene ◽  
Genomic Context ◽  
Male Individual ◽  
Long Read ◽  
Salix Purpurea ◽  
Populus Species

The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.

scholarly journals Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Brennan Hyden ◽  
Craig H. Carlson ◽  
Fred E. Gouker ◽  
Jeremy Schmutz ◽  
Kerrie Barry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sex Determination ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Small Rna Sequencing ◽  
Regulation Of Transcription ◽  
Eqtl Analysis ◽  
Sex Dimorphism ◽  
Network Analyses ◽  
Salix Purpurea

AbstractSex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

scholarly journals Towards a better understanding of the low recall of insertion variants with short-read based variant callers

2020 ◽  
Author(s):  
Wesley Delage ◽  
Julien Thevenon ◽  
Claire Lemaitre
Keyword(s):  
Gold Standard ◽  
Insertion Site ◽  
Structural Variants ◽  
Genomic Context ◽  
Breakpoint Junction ◽  
Short Read ◽  
Depth Analysis ◽  
Long Read ◽  
The Impact

AbstractSince 2009, numerous tools have been developed to detect structural variants (SVs) using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gold standard variant callsets. The advent of long read technologies has completely changed the situation. In 2019, two independent cross technologies studies have published the most complete variant callsets with sequence resolved insertions in human individuals. Among the reported insertions, only 17 to 37% could be discovered with short-read based tools. In this work, we performed an in-depth analysis of these unprecedented insertion callsets in order to investigate the causes of such failures. We have first established a precise classification of insertion variants according to four layers of characterization: the nature and size of the inserted sequence, the genomic context of the insertion site and the breakpoint junction complexity. Because these levels are intertwined, we then used simulations to characterize the impact of each complexity factor on the recall of several SV callers. Simulations showed that the most impacting factor was the insertion type rather than the genomic context, with various difficulties being handled differently among the tested SV callers, and they highlighted the lack of sequence resolution for most insertion calls. Our results explain the low recall by pointing out several difficulty factors among the observed insertion features and provide avenues for improving SV caller algorithms and their [email protected]

scholarly journals Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly

2020 ◽  
Author(s):  
Xuefang Zhao ◽  
Ryan L. Collins ◽  
Wan-Ping Lee ◽  
Alexandra M. Weber ◽  
Yukyung Jun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Human Genetics ◽  
Clinical Diagnostics ◽  
Added Value ◽  
Mendelian Disease ◽  
Segmental Duplications ◽  
Genomic Context ◽  
Long Read

AbstractVirtually all genome sequencing efforts in national biobanks, complex and Mendelian disease programs, and emerging clinical diagnostic approaches utilize short-reads (srWGS), which present constraints for genome-wide discovery of structural variants (SVs). Alternative long-read single molecule technologies (lrWGS) offer significant advantages for genome assembly and SV detection, while these technologies are currently cost prohibitive for large-scale disease studies and clinical diagnostics (∼5-12X higher cost than comparable coverage srWGS). Moreover, only dozens of such genomes are currently publicly accessible by comparison to millions of srWGS genomes that have been commissioned for international initiatives. Given this ubiquitous reliance on srWGS in human genetics and genomics, we sought to characterize and quantify the properties of SVs accessible to both srWGS and lrWGS to establish benchmarks and expectations in ongoing medical and population genetic studies, and to project the added value of SVs uniquely accessible to each technology. In analyses of three trios with matched srWGS and lrWGS from the Human Genome Structural Variation Consortium (HGSVC), srWGS captured ∼11,000 SVs per genome using reference-based algorithms, while haplotype-resolved assembly from lrWGS identified ∼25,000 SVs per genome. Detection power and precision for SV discovery varied dramatically by genomic context and variant class: 9.7% of the current GRCh38 reference is defined by segmental duplications (SD) and simple repeats (SR), yet 91.4% of deletions that were specifically discovered by lrWGS localized to these regions. Across the remaining 90.3% of the human reference, we observed extremely high concordance (93.8%) for deletions discovered by srWGS and lrWGS after error correction using the raw lrWGS reads. Conversely, lrWGS was superior for detection of insertions across all genomic contexts. Given that the non-SD/SR sequences span 90.3% of the GRCh38 reference, and encompass 95.9% of coding exons in currently annotated disease associated genes, improved sensitivity from lrWGS to discover novel and interpretable pathogenic deletions not already accessible to srWGS is likely to be incremental. However, these analyses highlight the added value of assembly-based lrWGS to create new catalogues of functional insertions and transposable elements, as well as disease associated repeat expansions in genomic regions previously recalcitrant to routine assessment.

Sex determination of forensic samples by dual PCR amplification of an X-Y homologous gene

1992 ◽  
Vol 52 (2) ◽  
pp. 143-148 ◽  
Author(s):  
Atsushi Akane ◽  
Satoko Seki ◽  
Hiroshi Shiono ◽  
Hiroaki Nakamura ◽  
Masanori Hasegawa ◽  
...  
Keyword(s):  
Sex Determination ◽  
Pcr Amplification ◽  
Homologous Gene ◽  
Forensic Samples

scholarly journals Comprehensive mutagenesis of thefimSpromoter regulatory switch reveals novel regulation of type 1 pili in uropathogenicEscherichia coli

2016 ◽  
Vol 113 (15) ◽  
pp. 4182-4187 ◽  
Author(s):  
Huibin Zhang ◽  
Teodorus T. Susanto ◽  
Yue Wan ◽  
Swaine L. Chen
Keyword(s):  
Phase Variation ◽  
Inverted Repeats ◽  
Phase Variable ◽  
Genomic Context ◽  
Clonal Population ◽  
Control Phase ◽  
Additional Layer ◽  
Type 1 Pili ◽  
Tract Infections

Type 1 pili (T1P) are major virulence factors for uropathogenicEscherichia coli(UPEC), which cause both acute and recurrent urinary tract infections. T1P expression therefore is of direct relevance for disease. T1P are phase variable (both piliated and nonpiliated bacteria exist in a clonal population) and are controlled by an invertible DNA switch (fimS), which contains the promoter for thefimoperon encoding T1P. Inversion offimSis stochastic but may be biased by environmental conditions and other signals that ultimately converge atfimSitself. Previous studies offimSsequences important for T1P phase variation have focused on laboratory-adaptedE.colistrains and have been limited in the number of mutations or by alteration of thefimSgenomic context. We surmounted these limitations by using saturating genomic mutagenesis offimScoupled with accurate sequencing to detect both mutations and phase status simultaneously. In addition to the sequences known to be important for biasingfimSinversion, our method also identifies a previously unknown pair of 5′ UTR inverted repeats that act by altering the relativefimAlevels to control phase variation. Thus we have uncovered an additional layer of T1P regulation potentially impacting virulence and the coordinate expression of multiple pilus systems.

scholarly journals Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method

2019 ◽  
Author(s):  
Weiwen Wang ◽  
Robert Lanfear
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Land Plant ◽  
Inverted Repeats ◽  
Equal Frequency ◽  
Large Single Copy ◽  
Chloroplast Genomes ◽  
Long Read ◽  
Small Single Copy ◽  
Large Single Copy Region

AbstractThe chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labour-intensive, and this phenomenon remains understudied. Here we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.Significance StatementChloroplast genome consists of a large single copy region, a small single copy region, and two inverted repeats. Some decades ago, a discovery showed that there are two types chloroplast genome in some plants, which differ the way that the four regions are put together. However, this phenomenon has been shown in just a small number of species, and many open questions remain. Here, we develop a fast method to measure the chloroplast genome structures, based on long-reads. We show that almost all plants we analysed contain two possible genome structures, while a few plants contain only one structure. Our findings hint at the causes of the phenomenon, and provide a convenient new method with which to make rapid progress.

scholarly journals Integrative genomics reveals paths to sex dimorphism in Salix purpurea L.

2021 ◽  
Author(s):  
Brennan Hyden ◽  
Craig H. Carlson ◽  
Fred E. Gouker ◽  
Jeremy Schmutz ◽  
Kerrie Barry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sex Determination ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Small Rna Sequencing ◽  
Regulation Of Transcription ◽  
Eqtl Analysis ◽  
Sex Dimorphism ◽  
Network Analyses ◽  
Salix Purpurea

AbstractSex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

scholarly journals PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingli Yang ◽  
Wanqiu Lv ◽  
Liying Shao ◽  
Yanrui Fu ◽  
Haimei Liu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Cold Stress ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Intron Retention ◽  
Global Analysis ◽  
Populus Trichocarpa ◽  
Rna Seq ◽  
Long Read

In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.

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