scholarly journals The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

2019 ◽  
Author(s):  
Eric L. Patterson ◽  
Christopher A. Saski ◽  
Daniel B. Sloan ◽  
Patrick J. Tranel ◽  
Philip Westra ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Draft Genome ◽  
Mobile Element ◽  
Artificial Chromosome ◽  
Duplication Event ◽  
Kochia Scoparia ◽  
Tandem Gene Duplication ◽  
Draft Genome Assembly ◽  
Resistance Evolution ◽  
Gene Copies

ABSTRACTIncreased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world’s most-used herbicide. There are typically three to eight EPSPS copies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled the EPSPS locus from a glyphosate-resistant kochia plant by sequencing a kochia bacterial artificial chromosome library. These resources helped reconstruct the history of duplication in the structurally complex EPSPS locus and uncover the genes that are co-duplicated with EPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. We discovered a FHY3/FAR1-like mobile genetic element that is associated with the duplicated EPSPS gene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of the EPSPS gene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.

scholarly journals The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

2019 ◽  
Vol 11 (10) ◽  
pp. 2927-2940 ◽  
Author(s):  
Eric L Patterson ◽  
Christopher A Saski ◽  
Daniel B Sloan ◽  
Patrick J Tranel ◽  
Philip Westra ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Draft Genome ◽  
Mobile Element ◽  
Artificial Chromosome ◽  
Duplication Event ◽  
Kochia Scoparia ◽  
Tandem Gene Duplication ◽  
Artificial Chromosomes ◽  
Resistance Evolution ◽  
Epsps Gene

Abstract Increased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world’s most-used herbicide. There are typically three to eight EPSPS copies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled the EPSPS locus from a glyphosate-resistant kochia plant by sequencing select bacterial artificial chromosomes from a kochia bacterial artificial chromosome library. Comparing the resistant and susceptible EPSPS locus allowed us to reconstruct the history of duplication in the structurally complex EPSPS locus and uncover the genes that are coduplicated with EPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. Additionally, we discovered a mobile genetic element with a FHY3/FAR1-like gene predicted in its sequence that is associated with the duplicated EPSPS gene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of the EPSPS gene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.

scholarly journals Patterns of gene evolution following duplications and speciations in vertebrates

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8813 ◽  
Author(s):  
Kyle T. David ◽  
Jamie R. Oaks ◽  
Kenneth M. Halanych
Keyword(s):  
Gene Duplication ◽  
Gene Evolution ◽  
Strong Support ◽  
Duplication Event ◽  
Gene Trees ◽  
Loss Of Function ◽  
Eukaryotic Genes ◽  
Gene Copies ◽  
Duplication Events ◽  
And Function

Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

scholarly journals Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Bhavani Manivannan ◽  
Niranjana Mahalingam ◽  
Sudhir Jadhao ◽  
Amrita Mishra ◽  
Pravin Nilawe ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Genome Assembly ◽  
Biofilm Formation ◽  
Draft Genome ◽  
Drug Resistant ◽  
Draft Genome Assembly ◽  
Extensively Drug Resistant ◽  
History Of ◽  
Urinary Tuberculosis

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

scholarly journals Identification of members of the P-glycoprotein multigene family.

1989 ◽  
Vol 9 (3) ◽  
pp. 1224-1232 ◽  
Author(s):  
W F Ng ◽  
F Sarangi ◽  
R L Zastawny ◽  
L Veinot-Drebot ◽  
V Ling
Keyword(s):  
Multidrug Resistance ◽  
Gene Duplication ◽  
Gene Family ◽  
Multigene Family ◽  
Rhesus Monkeys ◽  
Genomic Library ◽  
Duplication Event ◽  
Glycoprotein Gene ◽  
P Glycoprotein ◽  
Exon Probe

Overproduction of P-glycoprotein is intimately associated with multidrug resistance. This protein appears to be encoded by a multigene family. Thus, differential expression of different members of this family may contribute to the complexity of the multidrug resistance phenotype. Three lambda genomic clones isolated from a hamster genomic library represent different members of the hamster P-glycoprotein gene family. Using a highly conserved exon probe, we found that the hamster P-glycoprotein gene family consists of three genes. We also found that the P-glycoprotein gene family consists of three genes in mice but has only two genes in humans and rhesus monkeys. The hamster P-glycoprotein genes have similar exon-intron organizations within the 3' region encoding the cytoplasmic domains. We propose that the hamster P-glycoprotein gene family arose from gene duplication. The hamster pgp1 and pgp2 genes appear to be more closely related to each other than either gene is to the pgp3 gene. We speculate that the hamster pgp1 and pgp2 genes arose from a recent gene duplication event and that primates did not undergo this duplication and therefore contain only two P-glycoprotein genes.

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

2012 ◽  
Vol 71 (6) ◽  
pp. 895-906 ◽  
Author(s):  
Luming Yang ◽  
Dal-Hoe Koo ◽  
Yuhong Li ◽  
Xuejiao Zhang ◽  
Feishi Luan ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Genome Assembly ◽  
Draft Genome ◽  
High Density ◽  
Chromosome Rearrangements ◽  
Draft Genome Assembly

A new aminopeptidase from diamondback moth provides evidence for a gene duplication event in Lepidoptera

1999 ◽  
Vol 8 (2) ◽  
pp. 171-177 ◽  
Author(s):  
W. X. Z. Chang ◽  
L. J. Gahan ◽  
B. E. Tabashnik ◽  
D. G. Heckel
Keyword(s):  
Gene Duplication ◽  
Diamondback Moth ◽  
Duplication Event ◽  
Gene Duplication Event

scholarly journals First draft genome of loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish

2021 ◽  
Author(s):  
Zhijin Liu ◽  
Xuekun Qian ◽  
Ziming Wang ◽  
Huamei Wen ◽  
Ling Han ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Eye Development ◽  
Draft Genome ◽  
Evolutionary Process ◽  
Integrated Approach ◽  
Sequencing Data ◽  
Retina Development ◽  
Draft Genome Assembly ◽  
Surface Dwelling

Abstract BcakgroundLoaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for research into the evolution of cavefishes.ResultsHere we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately 515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. We also performed genome re-sequencing of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O. daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype.ConclusionsWe here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).

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 Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

2021 ◽  
Author(s):  
Roger Huerlimann ◽  
Jeff A Cowley ◽  
Nicholas M Wade ◽  
Yinan Wang ◽  
Naga Kasinadhuni ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Protein Coding ◽  
Black Tiger Shrimp ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Tiger Shrimp ◽  
Endogenous Viral Elements

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of conjoined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

scholarly journals Target-Site Mutations and Expression of ALS Gene Copies Vary According to Echinochloa Species

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1841
Author(s):  
Silvia Panozzo ◽  
Elisa Mascanzoni ◽  
Laura Scarabel ◽  
Andrea Milani ◽  
Giliardi Dalazen ◽  
...  
Keyword(s):  
Cropping Systems ◽  
Point Mutations ◽  
Common Species ◽  
Target Site ◽  
The Other ◽  
Gene Copy ◽  
Resistance Level ◽  
Resistance Evolution ◽  
Gene Copies ◽  
Als Inhibitors

The sustainability of rice cropping systems is jeopardized by the large number and variety of populations of polyploid Echinochloa spp. resistant to ALS inhibitors. Better knowledge of the Echinochloa species present in Italian rice fields and the study of ALS genes involved in target-site resistance could significantly contribute to a better understanding of resistance evolution and management. Using a CAPS-rbcL molecular marker, two species, E. crus-galli (L.) P. Beauv. and E. oryzicola (Vasinger) Vasing., were identified as the most common species in rice in Italy. Mutations involved in ALS inhibitor resistance in the different species were identified and associated with the ALS homoeologs. The relative expression of the ALS gene copies was evaluated. Molecular characterization led to the identification of three ALS genes in E. crus-galli and two in E. oryzicola. The two species also carried different point mutations conferring resistance: Ala122Asn in E. crus-galli and Trp574Leu in E. oryzicola. Mutations were carried in the same gene copy (ALS1), which was significantly more expressed than the other copies (ALS2 and ALS3) in both species. These results explain the high resistance level of these populations and why mutations in the other ALS copies are not involved in herbicide resistance.

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