scholarly journals Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 213
Author(s):  
Flavia Angela Maria Maggiolini ◽  
Ludovica Mercuri ◽  
Francesca Antonacci ◽  
Fabio Anaclerio ◽  
Francesco Maria Calabrese ◽  
...  
Keyword(s):  
Gene Family ◽  
Single Molecule ◽  
Copy Number ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Specific Gene ◽  
Segmental Duplications ◽  
Chromosomal Distribution ◽  
High Sequence Identity ◽  
Specific Expression

POTE (prostate, ovary, testis, and placenta expressed) genes belong to a primate-specific gene family expressed in prostate, ovary, and testis as well as in several cancers including breast, prostate, and lung cancers. Due to their tumor-specific expression, POTEs are potential oncogenes, therapeutic targets, and biomarkers for these malignancies. This gene family maps within human and primate segmental duplications with a copy number ranging from two to 14 in different species. Due to the high sequence identity among the gene copies, specific efforts are needed to assemble these loci in order to correctly define the organization and evolution of the gene family. Using single-molecule, real-time (SMRT) sequencing, in silico analyses, and molecular cytogenetics, we characterized the structure, copy number, and chromosomal distribution of the POTE genes, as well as their expression in normal and disease tissues, and provided a comparative analysis of the POTE organization and gene structure in primate genomes. We were able, for the first time, to de novo sequence and assemble a POTE tandem duplication in marmoset that is misassembled and collapsed in the reference genome, thus revealing the presence of a second POTE copy. Taken together, our findings provide comprehensive insights into the evolutionary dynamics of the primate-specific POTE gene family, involving gene duplications, deletions, and long interspersed nuclear element (LINE) transpositions to explain the actual repertoire of these genes in human and primate genomes.

scholarly journals The hominoid-specific gene DSCR4 is involved in regulation of human leukocyte migration

2017 ◽  
Author(s):  
Morteza Mahmoudi Saber ◽  
Marziyeh Karimiavargani ◽  
Nilmini Hettiarachchi ◽  
Michiaki Hamada ◽  
Takanori Uzawa ◽  
...  
Keyword(s):  
Down Syndrome ◽  
Immune System ◽  
Neural Crest ◽  
De Novo ◽  
Human Leukocyte ◽  
Neural Crest Cells ◽  
Human Cells ◽  
Specific Gene ◽  
Facial Morphology ◽  
Specific Expression

AbstractDSCR4 (Down syndrome critical region 4) is an orphan retrotransposon-derived de-novo originated protein coding gene present only in hominoids (humans and great apes). Despite being located on the medically critical genomic region and abundance of evidences indicating its functionality, the role of this gene in human cells was utterly unknown. Due to absence of any prior knowledge regarding the function of DSCR4, for the first time here we used a gene-overexpression approach to discover biological importance and cellular roles of this gene. Our analysis strongly indicates DSCR4 to be mainly involved in regulation of the interconnected biological pathways related to cell migration, coagulation and immune system. We also showed that the predicted biological functions are consistent with tissue-specific expression of DSCR4 in migratory immune system leukocyte cells and neural crest cells that shape facial morphology of human embryo. Immune system and neural crest cells are also shown to be affected in Down syndrome patients who suffer from the same type of DSCR4 misregulation as in our study which further support our findings. Providing evidence for the critical roles of DSCR4 in human cells, our findings establish the basis for further investigations on the roles of DSCR4 in etiology of Down syndrome and unique characteristics of hominoids.

scholarly journals Genome-Wide Identification and Analysis of the NPR1-Like Gene Family in Bread Wheat and Its Relatives

2019 ◽  
Vol 20 (23) ◽  
pp. 5974 ◽  
Author(s):  
Xian Liu ◽  
Zhiguo Liu ◽  
Xinhui Niu ◽  
Qian Xu ◽  
Long Yang
Keyword(s):  
Gene Family ◽  
Bread Wheat ◽  
Plant Immunity ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Aegilops Tauschii ◽  
Regulatory Elements ◽  
Protein Domain ◽  
Chromosomal Distribution ◽  
Specific Expression

NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1), and its paralogues NPR3 and NPR4, are bona fide salicylic acid (SA) receptors and play critical regulatory roles in plant immunity. However, comprehensive identification and analysis of the NPR1-like gene family had not been conducted so far in bread wheat and its relatives. Here, a total of 17 NPR genes in Triticum aestivum, five NPR genes in Triticum urartu, 12 NPR genes in Triticum dicoccoides, and six NPR genes in Aegilops tauschii were identified using bioinformatics approaches. Protein properties of these putative NPR1-like genes were also described. Phylogenetic analysis showed that the 40 NPR1-like proteins, together with 40 NPR1-related proteins from other plant species, were clustered into three major clades. The TaNPR1-like genes belonging to the same Arabidopsis subfamilies shared similar exon-intron patterns and protein domain compositions, as well as conserved motifs and amino acid residues. The cis-regulatory elements related to SA were identified in the promoter regions of TaNPR1-like genes. The TaNPR1-like genes were intensively mapped on the chromosomes of homoeologous groups 3, 4, and 5, except TaNPR2-D. Chromosomal distribution and collinearity analysis of NPR1-like genes among bread wheat and its relatives revealed that the evolution of this gene family was more conservative following formation of hexaploid wheat. Transcriptome data analysis indicated that TaNPR1-like genes exhibited tissue/organ-specific expression patterns and some members were induced under biotic stress. These findings lay the foundation for further functional characterization of NPR1-like proteins in bread wheat and its relatives.

scholarly journals High-Quality Assembly of an Individual of Yoruban Descent

2016 ◽  
Author(s):  
Karyn Meltz Steinberg ◽  
Tina Graves Lindsay ◽  
Valerie A. Schneider ◽  
Mark J.P. Chaisson ◽  
Chad Tomlinson ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Bac Library ◽  
Segmental Duplications ◽  
High Quality ◽  
Sequencing Technologies ◽  
Human Genomes ◽  
Genome Assemblies ◽  
Complete Genomic

ABSTRACTDe novo assembly of human genomes is now a tractable effort due in part to advances in sequencing and mapping technologies. We use PacBio single-molecule, real-time (SMRT) sequencing and BioNano genomic maps to construct the first de novo assembly of NA19240, a Yoruban individual from Africa. This chromosome-scaffolded assembly of 3.08 Gb with a contig N50 of 7.25 Mb and a scaffold N50 of 78.6 Mb represents one of the most contiguous high-quality human genomes. We utilize a BAC library derived from NA19240 DNA and novel haplotype-resolving sequencing technologies and algorithms to characterize regions of complex genomic architecture that are normally lost due to compression to a linear haploid assembly. Our results demonstrate that multiple technologies are still necessary for complete genomic representation, particularly in regions of highly identical segmental duplications. Additionally, we show that diploid assembly has utility in improving the quality of de novo human genome assemblies.

scholarly journals Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome

2018 ◽  
Author(s):  
Ching-Ho Chang ◽  
Amanda M. Larracuente
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Gene Conversion ◽  
Y Chromosome ◽  
Single Molecule ◽  
De Novo ◽  
High Rate ◽  
Genome Wide ◽  
Conversion Rates ◽  
Multiple Copies

ABSTRACTHeterochromatic regions of the genome are repeat-rich and gene poor, and are therefore underrepresented in even in the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9-Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family—crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.

scholarly journals The Dormancy Marker DRM1/ARP Associated with Dormancy but a Broader Role In Planta

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Georgina M. Rae ◽  
Karine David ◽  
Marion Wood
Keyword(s):  
Molecular Markers ◽  
Gene Family ◽  
Release Mechanism ◽  
Specific Gene ◽  
Dormancy Release ◽  
In Planta ◽  
High Sequence Identity ◽  
Growth Release ◽  
Sequence Identity ◽  
Wide Range

Plants must carefully regulate their development in order to survive a wide range of conditions. Of particular importance to this is dormancy release, deciding when to grow and when not to, given these varying conditions. In order to better understand the growth release mechanism of dormant tissue at the molecular and physiological levels, molecular markers can be used. One gene family that has a long association with dormancy, which is routinely used as a marker for dormancy release, is DRM1/ARP (dormancy-associated gene-1/auxin-repressed protein). This plant-specific gene family has high sequence identity at the protein level throughout several plant species, but its function in planta remains undetermined. This review brings together and critically analyzes findings on the DRM1/ARP family from a number of species. We focus on the relevance of this gene as a molecular marker for dormancy, raising questions of what its role might actually be in the plant.

scholarly journals Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Fan ◽  
Xiaobao Wei ◽  
Dili Lai ◽  
Hao Yang ◽  
Liang Feng ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Quantitative Polymerase Chain Reaction ◽  
Foxtail Millet ◽  
Fruit Weight ◽  
Segmental Duplications ◽  
Biotic And Abiotic Stress ◽  
Chromosomal Distribution ◽  
Phylogenetic Tree Analysis ◽  
Systematic Analysis

Abstract Background GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. Results In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. Conclusions Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.

scholarly journals High-throughput long paired-end sequencing of a Fosmid library by PacBio

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Zhaozhao Dai ◽  
Tong Li ◽  
Jiadong Li ◽  
Zhifei Han ◽  
Yonglong Pan ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Single Molecule ◽  
Genome Assembly ◽  
De Novo ◽  
Average Length ◽  
New Method ◽  
Segmental Duplications ◽  
Structural Rearrangements ◽  
De Novo Genome Assembly ◽  
Paired End Sequencing

Abstract Background Large insert paired-end sequencing technologies are important tools for assembling genomes, delineating associated breakpoints and detecting structural rearrangements. To facilitate the comprehensive detection of inter- and intra-chromosomal structural rearrangements or variants (SVs) and complex genome assembly with long repeats and segmental duplications, we developed a new method based on single-molecule real-time synthesis sequencing technology for generating long paired-end sequences of large insert DNA libraries. Results A Fosmid vector, pHZAUFOS3, was developed with the following new features: (1) two 18-bp non-palindromic I-SceI sites flank the cloning site, and another two sites are present in the skeleton of the vector, allowing long DNA inserts (and the long paired-ends in this paper) to be recovered as single fragments and the vector (~ 8 kb) to be fragmented into 2–3 kb fragments by I-SceI digestion and therefore was effectively removed from the long paired-ends (5–10 kb); (2) the chloramphenicol (Cm) resistance gene and replicon (oriV), necessary for colony growth, are located near the two sides of the cloning site, helping to increase the proportion of the paired-end fragments to single-end fragments in the paired-end libraries. Paired-end libraries were constructed by ligating the size-selected, mechanically sheared pooled Fosmid DNA fragments to the Ampicillin (Amp) resistance gene fragment and screening the colonies with Cm and Amp. We tested this method on yeast and Setaria italica Yugu1. Fosmid-size paired-ends with an average length longer than 2 kb for each end were generated. The N50 scaffold lengths of the de novo assemblies of the yeast and S. italica Yugu1 genomes were significantly improved. Five large and five small structural rearrangements or assembly errors spanning tens of bp to tens of kb were identified in S. italica Yugu1 including deletions, inversions, duplications and translocations. Conclusions We developed a new method for long paired-end sequencing of large insert libraries, which can efficiently improve the quality of de novo genome assembly and identify large and small structural rearrangements or assembly errors.

scholarly journals Genome-wide identification of the BASS gene family in four Gossypium species and functional characterization of GhBASSs against salt stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Thwin Myo ◽  
Fang Wei ◽  
Honghao Zhang ◽  
Jianfeng Hao ◽  
Bin Zhang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Gene Family ◽  
Sequence Similarity ◽  
Functional Characterization ◽  
Tetraploid Cotton ◽  
Segmental Duplications ◽  
Specific Expression ◽  
Cotton Species ◽  
Genome Duplications ◽  
Plant Salt Tolerance

AbstractBile acid sodium symporter (BASS) family proteins encode a class of sodium/solute symporters. Even though the sodium transporting property of BASSs in mammals was well studied, their sodium transportability and functional roles in plant salt tolerance remained largely unknown. Here, BASS family members from 4 cotton species, as well as 30 other species were identified. Then, they were designated as members of BASS1 to BASS5 subfamilies according to their sequence similarity and phylogenetic relationships. There were 8, 11, 16 and 18 putative BASS genes in four cotton species. While whole-genome duplications (WGD) and segmental duplications rendered the expansion of the BASS gene family in cotton, BASS gene losses occurred in the tetraploid cotton during the evolution from diploids to allotetraploids. Concerning functional characterizations, the transcript profiling of GhBASSs revealed that they not only preferred tissue-specific expression but also were differently induced by various stressors and phytohormones. Gene silencing and overexpression experiments showed that GhBASS1 and GhBASS3 positively regulated, whereas GhBASS2, GhBASS4 and GhBASS5 negatively regulated plant salt tolerance. Taken together, BASS family genes have evolved before the divergence from the common ancestor of prokaryotes and eukaryotes, and GhBASSs are plastidial sodium-dependent metabolite co-transporters that can influence plant salt tolerance.

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