scholarly journals Widespread imprinting of transposable elements and variable genes in the maize endosperm

PLoS Genetics ◽  
2021 ◽  
Vol 17 (4) ◽  
pp. e1009491
Author(s):  
Sarah N. Anderson ◽  
Peng Zhou ◽  
Kaitlin Higgins ◽  
Yaniv Brandvain ◽  
Nathan M. Springer
Keyword(s):  
Transposable Elements ◽  
Critical Time ◽  
Flowering Plant ◽  
Nucleotide Polymorphisms ◽  
Maternal Expression ◽  
Expression Of Genes ◽  
Using Data ◽  
Plant Life Cycle ◽  
Flowering Plant Species ◽  
Genome Assemblies

Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.

scholarly journals Widespread imprinting of transposable elements and young genes in the maize endosperm

2020 ◽  
Author(s):  
Sarah N Anderson ◽  
Peng Zhou ◽  
Kaitlin Higgins ◽  
Yaniv Brandvain ◽  
Nathan M Springer
Keyword(s):  
Transposable Elements ◽  
Critical Time ◽  
Flowering Plant ◽  
Nucleotide Polymorphisms ◽  
Maternal Expression ◽  
Expression Of Genes ◽  
Using Data ◽  
Plant Life Cycle ◽  
Flowering Plant Species ◽  
Genome Assemblies

AbstractFertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding the rate of turnover for gain or loss of imprinted expression has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene. Read alignments over maternal TE-gene pairs indicate fused transcripts, suggesting that variable TEs contribute imprinted expression of nearby genes.

scholarly journals Conserved and non-conserved triggers of 24-nt reproductive phasiRNAs in eudicots

2021 ◽  
Author(s):  
Suresh Pokhrel ◽  
Kun Huang ◽  
Blake C. Meyers
Keyword(s):  
Small Rnas ◽  
Reproductive Organs ◽  
Flowering Plant ◽  
Small Interfering Rnas ◽  
Expression Of Genes ◽  
Tapetal Cells ◽  
Wild Strawberry ◽  
Flowering Plant Species ◽  
Mother Cells ◽  
And Function

AbstractPlant small RNAs (sRNAs) play important roles in plant growth and development by modulating expression of genes and transposons. In many flowering plant species, male reproductive organs, the anthers, produce abundant phased small interfering RNAs (phasiRNAs). Two classes of reproductive phasiRNAs are generally known, mostly from monocots: pre-meiotic 21-nt phasiRNAs triggered by miR2118, and meiotic 24-nt phasiRNAs triggered by miR2275. Here, we describe conserved and non-conserved triggers of 24-nt phasiRNAs in several eudicots. We found that the abundant 24-nt phasiRNAs in the basal eudicot columbine are produced by the canonical trigger, miR2275, as well as by other non-conserved triggers, miR482/2118 and aco_cand81. These triggering miRNAs are localized in microspore mother cells (MMC) and tapetal cells of meiotic and post-meiotic stage anthers. Furthermore, we identified a new trigger (miR11308) of 24-nt phasiRNAs and an expanded number of 24-PHAS loci in wild strawberry. We validated the presence of miR2275-derived 24-nt phasiRNAs pathway in rose. Finally, we evaluated all the eudicots that have been validated for the presence of 24-nt phasiRNAs as models to study biogenesis and function of 24-nt phasiRNAs and conclude that columbine would be an excellent model because of its extensive number of 24-PHAS loci and its diversity of trigger miRNAs.

EpiPen: An R Package to Investigate Two-Locus Epistatic Models

2014 ◽  
Vol 17 (4) ◽  
Author(s):  
Raymond K. Walters ◽  
Charles Laurin ◽  
Gitta H. Lubke
Keyword(s):  
Power Analysis ◽  
R Package ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Model Interpretation ◽  
Genome Wide ◽  
Using Data ◽  
Power Analyses

Epistasis is a growing area of research in genome-wide studies, but the differences between alternative definitions of epistasis remain a source of confusion for many researchers. One problem is that models for epistasis are presented in a number of formats, some of which have difficult-to-interpret parameters. In addition, the relation between the different models is rarely explained. Existing software for testing epistatic interactions between single-nucleotide polymorphisms (SNPs) does not provide the flexibility to compare the available model parameterizations. For that reason we have developed an R package for investigating epistatic and penetrance models, EpiPen, to aid users who wish to easily compare, interpret, and utilize models for two-locus epistatic interactions. EpiPen facilitates research on SNP-SNP interactions by allowing the R user to easily convert between common parametric forms for two-locus interactions, generate data for simulation studies, and perform power analyses for the selected model with a continuous or dichotomous phenotype. The usefulness of the package for model interpretation and power analysis is illustrated using data on rheumatoid arthritis.

scholarly journals Frequent gain- and loss-of-function mutations of the BjMYB113 gene accounted for leaf color variation in Brassica juncea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Guanghui An ◽  
Jiongjiong Chen
Keyword(s):  
Brassica Juncea ◽  
Anthocyanin Biosynthesis ◽  
Color Variation ◽  
Nucleotide Polymorphisms ◽  
Loss Of Function ◽  
High Accumulation ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Promoter Sequences ◽  
Expression Of Genes

Abstract Background Mustard (Brassica juncea) is an important economic vegetable, and some cultivars have purple leaves and accumulate more anthocyanins than the green. The genetic and evolution of purple trait in mustard has not been well studied. Result In this study, free-hand sections and metabolomics showed that the purple leaves of mustard accumulated more anthocyanins than green ones. The gene controlling purple leaves in mustard, Mustard Purple Leaves (MPL), was genetically mapped and a MYB113-like homolog was identified as the candidate gene. We identified three alleles of the MYB113-like gene, BjMYB113a from a purple cultivar, BjMYB113b and BjMYB113c from green cultivars. A total of 45 single nucleotide polymorphisms (SNPs) and 8 InDels were found between the promoter sequences of the purple allele BjMYB113a and the green allele BjMYB113b. On the other hand, the only sequence variation between the purple allele BjMYB113a and the green allele BjMYB113c is an insertion of 1,033-bp fragment in the 3’region of BjMYB113c. Transgenic assay and promoter activity studies showed that the polymorphism in the promoter region was responsible for the up-regulation of the purple allele BjMYB113a and high accumulation of anthocyanin in the purple cultivar. The up-regulation of BjMYB113a increased the expression of genes in the anthocyanin biosynthesis pathway including BjCHS, BjF3H, BjF3’H, BjDFR, BjANS and BjUGFT, and consequently led to high accumulation of anthocyanin. However, the up-regulation of BjMYB113 was compromised by the insertion of 1,033-bp in 3’region of the allele BjMYB113c. Conclusions Our results contribute to a better understanding of the genetics and evolution of the BjMYB113 gene controlling purple leaves and provide useful information for further breeding programs of mustard.

scholarly journals Documentation of flora of Rara lake and adjoining areas in mid-western region of Nepal

2013 ◽  
Vol 21 (1) ◽  
pp. 41-47
Author(s):  
BK Basnet
Keyword(s):  
National Park ◽  
Secondary Data ◽  
Flowering Plant ◽  
Western Region ◽  
Ramsar Site ◽  
Secondary Sources ◽  
Data Field ◽  
Adjoining Area ◽  
Faunal Diversity ◽  
Flowering Plant Species

Rara National Park is the smallest national park of the country. It is rich in floral and faunal diversity. Rara is one of the sacred lakes and is listed as a Ramsar site. The aim of the study was to compile the representative flora of Rara lake and to present status of available vegetation. The research used both primary and secondary sources of data. Field visit was conducted in June, 2010 during which more than 300 plant specimens were collected. The secondary data were collected from Rara and adjoining area like Gamgadi. These data were thoroughly analyzed to understand the composition of vegetation. The study revealed the existence of about 224 flowering plant species in the area, under 173 genera and 67 families. Compositae was found to be the largest family (21 species and 17 genera) followed by Rosaceae (19 species and 10 genera). DOI: http://dx.doi.org/10.3126/banko.v21i1.9063 Banko Janakari, Vol. 21, No. 1 2011; 41-47

scholarly journals Role of Transposable Elements in Gene Regulation in the Human Genome

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 118
Author(s):  
Arsala Ali ◽  
Kyudong Han ◽  
Ping Liang
Keyword(s):  
Gene Regulation ◽  
Transposable Elements ◽  
Regulatory Sequences ◽  
Rna Sequences ◽  
Expression Of Genes ◽  
Wide Range ◽  
Lineage Specificity ◽  
Regulatory Rnas ◽  
Potential Factors ◽  
Interspersed Repeats

Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

scholarly journals The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

2016 ◽  
Author(s):  
Jian-Zhi Huang ◽  
Chih-Peng Lin ◽  
Ting-Chi Cheng ◽  
Ya-Wen Huang ◽  
Yi-Jung Tsai ◽  
...  
Keyword(s):  
Economic Value ◽  
Draft Genome ◽  
Floral Organ ◽  
Cool Temperature ◽  
Organ Development ◽  
Nucleotide Polymorphisms ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Genome Data ◽  
Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

scholarly journals Bmmp influences wing shape by regulating anterior-posterior and proximal-distal axis development

2021 ◽  
Author(s):  
Yunlong Zou ◽  
Xin Ding ◽  
Li Zhang ◽  
Lifeng Xu ◽  
Shubo Liang ◽  
...  
Keyword(s):  
Molecular Mapping ◽  
Wing Shape ◽  
Wing Development ◽  
Mrna Levels ◽  
Nucleotide Polymorphisms ◽  
Insect Wing ◽  
Expression Of Genes ◽  
Flight Capacity ◽  
Null Mutants ◽  
Anterior Posterior

Insect wings are subject to strong selective pressure, resulting in the evolution of remarkably diverse wing shapes that largely determine flight capacity. However, the genetic basis and regulatory mechanisms underlying wing shape development are not well understood. The silkworm Bombyx mori micropterous ( mp ) mutant exhibits shortened wing length and enlarged vein spacings , albeit without changes in total wing area. Thus, the mp mutant comprises a valuable genetic resource for studying wing shape development. In this study, we used molecular mapping to identify the gene responsible for the mp phenotype and designated it Bmmp . Phenotype-causing mutations were identified as indels and single nucleotide polymorphisms in non-coding regions. These mutations resulted in decreased Bmmp mRNA levels and changes in transcript isoform composition. Bmmp null mutants were generated by CRISPR/Cas9 and exhibited significantly smaller wings. By examining the expression of genes critical to wing development in wildtype and Bmmp null mutants, we found that Bm mp exerts its function by coordinately modulating anterior-posterior and proximal-distal axis development. We also studied a Drosophila mp mutant and found that Bmmp is functionally conserved in Drosophila . The Drosophila mp mutant strain exhibits curly wings of reduced size and a complete loss of flight capacity. Our results increase our understanding of the mechanisms underpinning insect wing development and reveal potential targets for pest control.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

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