scholarly journals Sequence Composition of Bacterial Chromosome Clones in a Transgressive Root-Knot Nematode Resistance Chromosome Region in Tetraploid Cotton

2020 ◽  
Vol 11 ◽  
Author(s):  
Congli Wang ◽  
Mauricio Ulloa ◽  
Robert L. Nichols ◽  
Philip A. Roberts
Keyword(s):  
Gene Annotation ◽  
Chromosome Region ◽  
Bac Library ◽  
Bacterial Chromosome ◽  
Homologous Region ◽  
Tetraploid Cotton ◽  
Root Knot Nematode ◽  
Homologous Segment ◽  
Rich Cluster ◽  
Sequence Composition

Plants evolve innate immunity including resistance genes to defend against pest and pathogen attack. Our previous studies in cotton (Gossypium spp.) revealed that one telomeric segment on chromosome (Chr) 11 in G. hirsutum cv. Acala NemX (rkn1 locus) contributed to transgressive resistance to the plant parasitic nematode Meloidogyne incognita, but the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a bacterial chromosome (BAC) library of Acala N901 (Acala NemX resistance source) was used to select, sequence, and analyze BAC clones associated with SSR markers in the complex rkn1 resistance region. Sequence alignment with the susceptible G. hirsutum cv. TM-1 genome indicated that 23 BACs mapped to TM-1-Chr11 and 18 BACs mapped to TM-1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (53–84%) mapped with the TM-1 genome in the rkn1 region on Chr 11 than to the homologous region (>89%) on Chr 21. A 3.1-cM genetic distance between the rkn1 flanking markers CIR316 and CIR069 was mapped in a Pima S-7 × Acala NemX RIL population with a physical distance ∼1 Mbp in TM-1. NCBI Blast and Gene annotation indicated that both Chr 11 and Chr 21 harbor resistance gene-rich cluster regions, but more multiple homologous copies of Resistance (R) proteins and of adjacent transposable elements (TE) are present within Chr 11 than within Chr 21. (CC)-NB-LRR type R proteins were found in the rkn1 region close to CIR316, and (TIR)-NB-LRR type R proteins were identified in another resistance rich region 10 cM from CIR 316 (∼3.1 Mbp in the TM-1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, multiple copies or duplication of R proteins, adjacent protein kinases, or TE in the rkn1 region on Chr 11 might be major factors contributing to complex recombination and transgressive resistance.

Replacement of α1-Na-K-ATPase of Dahl rats by Milan rats lowers blood pressure but does not affect its activity

2001 ◽  
Vol 7 (2) ◽  
pp. 171-177 ◽  
Author(s):  
SERGEI N. ORLOV ◽  
JULIE DUTIL ◽  
PAVEL HAMET ◽  
ALAN Y. DENG
Keyword(s):  
Blood Pressure ◽  
Quantitative Trait Locus ◽  
Atpase Activity ◽  
Quantitative Trait ◽  
Chromosome Region ◽  
Homologous Region ◽  
Congenic Strains ◽  
Baseline Activity ◽  
Trait Locus

Both linkage and use of congenic strains have shown that a chromosome region near the gene for the Na-K-ATPase α1-subunit ( Atp1a1) contained a quantitative trait locus (QTL) for blood pressure (BP). Currently, two congenic strains, designated S.M5 and S.M6, were made by replacing a segment of the Dahl salt-sensitive SS/Jr (S) rat by the homologous region of the Milan normotensive rat (MNS). In S.M5, the gene for Atp1a1 is from the MNS strain; whereas in S.M6, Atp1a1 is from the S strain. The baseline activity of the α1-Na-K-ATPase and its stoichiometry were evaluated by an assay of ouabain-sensitive inwardly and outwardly directed 86Rb and 22Na fluxes in erythrocytes. The two congenic strains showed a similar BP, but both had a BP lower than that of S rats ( P < 0.0001). Neither the α1-Na-K-ATPase activity nor its stoichiometry was affected by the substitution of the Atp1a1 alleles of S by those of MNS. Thus the BP-lowering effects observed in S.M5 and S.M6 could not be attributed to the α1-Na-K-ATPase activity or its stoichiometry. Atp1a1 is not supported as a candidate to be a BP QTL.

scholarly journals Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection

2020 ◽  
Vol 21 (3) ◽  
pp. 848
Author(s):  
Yuan Zhou ◽  
Di Zhao ◽  
Li Shuang ◽  
Dongxue Xiao ◽  
Yuanhu Xuan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Gene Annotation ◽  
Oryza Sativa L ◽  
Development Stage ◽  
Post Inoculation ◽  
Rna Seq ◽  
Wild Type ◽  
Root Knot Nematode ◽  
Rice Roots ◽  
Invasion Stage

Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.

scholarly journals Analysis of the 5'-upstream regions of the human relaxin H1 and H2 genes and their chromosomal localization on chromosome 9p24.1 by radiation hybrid and breakpoint mapping

1999 ◽  
Vol 23 (3) ◽  
pp. 355-365 ◽  
Author(s):  
JL Garibay-Tupas ◽  
K Csiszar ◽  
M Fox ◽  
S Povey ◽  
GD Bryant-Greenwood
Keyword(s):  
Radiation Hybrid ◽  
Regulatory Elements ◽  
Distal Region ◽  
Biologically Active ◽  
Evolutionary Significance ◽  
Homologous Region ◽  
Coding Region ◽  
Chromosomal Locus ◽  
Homologous Segment ◽  
Breakpoint Mapping

Relaxins are known endocrine and autocrine/paracrine hormones that play a major role in reproduction. In the human there are two relaxin genes, H1 and H2 which share 90% sequence homology within their coding region. The biological and evolutionary significance of two highly homologous and biologically active human relaxins is unknown. In order to achieve a better understanding of the regulatory mechanisms involved in the differential expression of these two genes and to gain insight into their role(s) in the preterm premature rupture of the membranes, we have investigated the properties of their 5'-upstream regions and mapped them both by radiation hybrid and breakpoint mapping into the same chromosome 9p24.1 locus. The 5' ends of these relaxin genes could be divided into a proximal highly homologous segment and a distal non-homologous region. Within the proximal region are contained several putative regulatory elements common to both genes, suggesting a similar regulatory mechanism. The clustering of the relaxin genes within the same chromosomal locus suggests that these genes may be under a common regulation. On the other hand, a distinct gene-specific regulation may also exist for the individual relaxin genes since cis elements specific to each gene were identified at their 5' ends. Moreover, the observed divergence at the distal region of their 5'-upstream sequences may provide the structural features that act as gene-specific transcription regulators. Since the two genes are highly homologous in both their coding and flanking regions, the divergence at the distal region of their 5' ends may be important in the regulation of these genes and in their involvement in the pathology of preterm birth.

Identification of Fetuin-B as a member of a cystatin-like gene family on mouse chromosome 16 with tumor suppressor activity

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 931-946 ◽  
Author(s):  
Ssucheng J Hsu ◽  
Hiroki Nagase ◽  
Allan Balmain
Keyword(s):  
Mouse Chromosome ◽  
Chromosome Region ◽  
Tumor Development ◽  
Bac Library ◽  
Mouse Skin ◽  
Proximal Region ◽  
Skin Tumor ◽  
Chromosome 16 ◽  
Suppressor Activity ◽  
Squamous Carcinoma Cells

Studies of mouse models for multistage carcinogenesis have led to the identification of a susceptibility locus for skin tumor development (Skts9) in the proximal region of mouse chromosome 16. This chromosome region shows a loss of heterozygosity or an allelic imbalance in mouse skin and pancreatic islet carcinoma, and has been associated with angiogenesis. The microsatellite marker D16Mit2, which has the strongest linkage to skin tumor susceptibility, was used to screen a bacterial artificial chromosome (BAC) library, leading to the identification of the histidine-rich glycoprotein (Hrg) and Fetuin-B as the most tightly linked genes. These genes are members of a cystatin-like superfamily that includes the neighboring genes Kng and Ahsg/Fetuin. Overexpression of Fetuin-B in skin squamous carcinoma cells led to suppression of tumor growth in nude mice. The neighboring genes Kng and Ahsg also have potential roles in angiogenesis and (or) tumor development, and several genes in this locus may be candidates for the Skts9 gene.Key words: Skts9, Hrg, Fetuin-B, cystatin-like superfamily.

Sequence composition and organization in the Sh2/A1-homologous region of rice

1996 ◽  
Vol 32 (6) ◽  
pp. 999-1001 ◽  
Author(s):  
Mingsheng Chen ◽  
Jeffrey L. Bennetzen
Keyword(s):  
Homologous Region ◽  
Sequence Composition

High-throughput targeted SSR marker development in peach (Prunus persica)

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 319-328 ◽  
Author(s):  
Ying Wang ◽  
Laura L Georgi ◽  
Tatyana N Zhebentyayeva ◽  
Gregory L Reighard ◽  
Ralph Scorza ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
High Throughput ◽  
Prunus Persica ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Nematode Resistance ◽  
Regions Of Interest ◽  
Mapping Technique ◽  
Root Knot Nematode ◽  
Ssr Loci

Simple sequence repeats (SSRs) have proven to be highly polymorphic, easily reproducible, codominant markers. However, developing an SSR map is very time consuming and expensive, and most SSRs are not specifically linked to gene loci of immediate interest. The ideal situation would be to combine a high-throughput, relatively inexpensive mapping technique with rapid identification of SSR loci in mapped regions of interest. For this reason, we coupled the high-throughput technique of AFLP mapping with subsequent direct targeting of SSRs identified in AFLP-marked regions of interest. This approach relied on the availability of peach bacterial artificial chromosome (BAC) library resources. We present examples of using this strategy to rapidly identify SSR loci tightly linked to two important, simply inherited traits in peach (Prunus persica (L.) Batsch): root-knot nematode resistance and control of the evergrowing trait. SSRs developed in this study were also tested for their transportability in other Prunus species and in apricots.Key words: bacterial artificial chromosome, apricot, molecular markers, Meloidogyne spp., evergrowing gene.

scholarly journals Ambiguous splice sites distinguish circRNA and linear splicing in the human genome

2018 ◽  
Vol 35 (8) ◽  
pp. 1263-1268 ◽  
Author(s):  
Roozbeh Dehghannasiri ◽  
Linda Szabo ◽  
Julia Salzman
Keyword(s):  
Ab Initio ◽  
Rna Splicing ◽  
Genomic Sequence ◽  
Gene Annotation ◽  
Null Distribution ◽  
Full Length ◽  
Supplementary Information ◽  
Splice Sites ◽  
Sequence Composition ◽  
Rna Transcripts

Abstract Motivation Identification of splice sites is critical to gene annotation and to determine which sequences control circRNA biogenesis. Full-length RNA transcripts could in principle complete annotations of introns and exons in genomes without external ontologies, i.e., ab initio. However, whether it is possible to reconstruct genomic positions where splicing occurs from full-length transcripts, even if sampled in the absence of noise, depends on the genome sequence composition. If it is not, there exist provable limits on the use of RNA-Seq to define splice locations (linear or circular) in the genome. Results We provide a formal definition of splice site ambiguity due to the genomic sequence by introducing equivalent junction, which is the set of local genomic positions resulting in the same RNA sequence when joined through RNA splicing. We show that equivalent junctions are prevalent in diverse eukaryotic genomes and occur in 88.64% and 78.64% of annotated human splice sites in linear and circRNA junctions, respectively. The observed fractions of equivalent junctions and the frequency of many individual motifs are statistically significant when compared against the null distribution computed via simulation or closed-form. The frequency of equivalent junctions establishes a fundamental limit on the possibility of ab initio reconstruction of RNA transcripts without appealing to the ontology of “GT-AG” boundaries defining introns. Said differently, completely ab initio is impossible in the vast majority of splice sites in annotated circRNAs and linear transcripts. Availability and implementation Two python scripts generating an equivalent junction sequence per junction are available at: https://github.com/salzmanlab/Equivalent-Junctions. Supplementary information Supplementary data are available at Bioinformatics online.

Bacterial artificial chromosome clones randomly selected for sequencing reveal genomic differences between soybean cultivars

2018 ◽  
Vol 69 (2) ◽  
pp. 131
Author(s):  
Tingting He ◽  
Longshu Yang ◽  
Xianlong Ding ◽  
Linfeng Chen ◽  
Yanwei Li ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Complete Sequence ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Bac Clones

This study pioneered the use of multiple technologies to combine the bacterial artificial chromosome (BAC) pooling strategy with high-throughput next- and third-generation sequencing technologies to analyse genomic difference. To understand the genetic background of the Chinese soybean cultivar N23601, we built a BAC library and sequenced 10 randomly selected clones followed by de novo assembly. Comparative analysis was conducted against the reference genome of Glycine max var. Williams 82 (2.0). Therefore, our result is an assessment of the reference genome. Our results revealed that 3517 single nucleotide polymorphisms (SNPs) and 662 insertion–deletions (InDels) occurred in ~1.2 Mb of the genomic region and that four of the 10 BAC clones contained 15 large structural variations (72 887 bp) compared with the reference genome. Gene annotation of the reference genome showed that Glyma.18g181000 was missing from the corresponding position of the 10 BAC clones. Additionally, there may be a problem with the assembly of some positions of the reference genome. Several gap regions in the reference genome could be supplemented by using the complete sequence of the 10 BAC clones. We believe that accurate and complete BAC sequence is a valuable resource that contributes to the completeness of the reference genome.

Repair pathway choice for double-strand breaks

2020 ◽  
Vol 64 (5) ◽  
pp. 765-777 ◽  
Author(s):  
Yixi Xu ◽  
Dongyi Xu
Keyword(s):  
Cell Cycle ◽  
Double Strand Breaks ◽  
Homologous Region ◽  
Gene Repair ◽  
Repair Pathway ◽  
Dna Double Strand Breaks ◽  
Environmental Radiation ◽  
Strand Breaks ◽  
Dna End Resection ◽  
End Resection

Abstract Deoxyribonucleic acid (DNA) is at a constant risk of damage from endogenous substances, environmental radiation, and chemical stressors. DNA double-strand breaks (DSBs) pose a significant threat to genomic integrity and cell survival. There are two major pathways for DSB repair: nonhomologous end-joining (NHEJ) and homologous recombination (HR). The extent of DNA end resection, which determines the length of the 3′ single-stranded DNA (ssDNA) overhang, is the primary factor that determines whether repair is carried out via NHEJ or HR. NHEJ, which does not require a 3′ ssDNA tail, occurs throughout the cell cycle. 53BP1 and the cofactors PTIP or RIF1-shieldin protect the broken DNA end, inhibit long-range end resection and thus promote NHEJ. In contrast, HR mainly occurs during the S/G2 phase and requires DNA end processing to create a 3′ tail that can invade a homologous region, ensuring faithful gene repair. BRCA1 and the cofactors CtIP, EXO1, BLM/DNA2, and the MRE11–RAD50–NBS1 (MRN) complex promote DNA end resection and thus HR. DNA resection is influenced by the cell cycle, the chromatin environment, and the complexity of the DNA end break. Herein, we summarize the key factors involved in repair pathway selection for DSBs and discuss recent related publications.

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