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Your search keyword '"Lineage-specific duplications"' showing total 5 results
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5 results on '"Lineage-specific duplications"'

1. Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species.

Author

Zhong, Yan, Chen, Zhao, and Cheng, Zong-Ming

Subjects
*PRUNUS, *CHROMOSOME duplication, *PLANT genes, *GENE families, *GENES, *SPECIES, *GENE libraries
Abstract

In this study, genome-wide identification, phylogenetic relationships, duplication time and selective pressure of the NBS-LRR genes, an important group of plant disease-resistance genes (R genes), were performed to uncover their genetic evolutionary patterns in the six Prunus species. A total of 1946 NBS-LRR genes were identified; specifically, 589, 361, 284, 281, 318, and 113 were identified in Prunus yedoensis, P. domestica, P. avium, P. dulcis, P. persica and P. yedoensis var. nudiflora, respectively. Two NBS-LRR gene subclasses, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (non-TNL), were also discovered. In total, 435 TNL and 1511 non-TNL genes were identified and could be classified into 30/55/75 and 103/158/191 multi-gene families, respectively, according to three different criteria. Higher Ks and Ka/Ks values were detected in TNL gene families than in non-TNL gene families. These results indicated that the TNL genes had more members involved in relatively ancient duplications and were affected by stronger selection pressure than the non-TNL genes. In general, the NBS-LRR genes were shaped by species-specific duplications, and lineage-specific duplications occurred at recent and relatively ancient periods among the six Prunus species. Therefore, different duplicated copies of NBS-LRRs can resist specific pathogens and will provide an R-gene library for resistance breeding in Prunus species. [ABSTRACT FROM AUTHOR]

Published
2022
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2. Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species

Author

Yan Zhong, Zhao Chen, and Zong-Ming Cheng

Subjects
Time Factors, Lineage-specific duplications, Genetic Speciation, Genes, Plant, Leucine-Rich Repeat Proteins, Evolution, Molecular, Prunus species, Species Specificity, Gene Expression Regulation, Plant, Gene Duplication, Genetics, Molecular Biology, Phylogeny, Disease Resistance, Plant Diseases, Plant Proteins, Disease resistance genes, Species-specific duplications, fungi, food and beverages, General Medicine, Multigene Family, Original Article, Prunus, Genome, Plant, NBS-LRR genes
Abstract

In this study, genome-wide identification, phylogenetic relationships, duplication time and selective pressure of the NBS-LRR genes, an important group of plant disease-resistance genes (R genes), were performed to uncover their genetic evolutionary patterns in the six Prunus species. A total of 1946 NBS-LRR genes were identified; specifically, 589, 361, 284, 281, 318, and 113 were identified in Prunus yedoensis, P. domestica, P. avium, P. dulcis, P. persica and P. yedoensis var. nudiflora, respectively. Two NBS-LRR gene subclasses, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (non-TNL), were also discovered. In total, 435 TNL and 1511 non-TNL genes were identified and could be classified into 30/55/75 and 103/158/191 multi-gene families, respectively, according to three different criteria. Higher Ks and Ka/Ks values were detected in TNL gene families than in non-TNL gene families. These results indicated that the TNL genes had more members involved in relatively ancient duplications and were affected by stronger selection pressure than the non-TNL genes. In general, the NBS-LRR genes were shaped by species-specific duplications, and lineage-specific duplications occurred at recent and relatively ancient periods among the six Prunus species. Therefore, different duplicated copies of NBS-LRRs can resist specific pathogens and will provide an R-gene library for resistance breeding in Prunus species.

Published
2021

3. Recurrent duplication-driven transposition of DNA during hominoid evolution.

Author

Johnson, Matthew E., Ze Cheng, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., Green, Eric D., and Eichier, Evan E.

Subjects
*CHROMOSOMAL translocation, *DNA, *HOMINIDS, *EVOLUTIONARY theories, *CHROMOSOMES, *GENETICS
Abstract

The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes. we show that a particular segmental duplication (LCR16a) has been the source locus for the formation of the majority of intrachromosomal duplications blocks on human chromosome 16. We provide evidence that this particular segment has been active independently in each great ape and human lineage at different points during evolution. Euchromatic sequence that flanks sites of LCR16a integration are frequently lineage-specific duplications. This process has mobilized duplication blocks (15ߝ200 kb in size) to new genomic locations in each species. Breakpoint analysis of lineage-specific insertions suggests coordinated deletion of repeat-rich DNA at the target site, in some cases deleting genes in that species. Our data support a model of duplication where the probability that a segment of DNA becomes duplicated is determined by its proximity to core duplicons, such as LCR16a. [ABSTRACT FROM AUTHOR]

Published
2006
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4. Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

Author

Eisen, Jonathan A., Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., Badger, Jonathan H., Ren, Qinghu, Amedeo, Paolo, Jones, Kristie M., Tallon, Luke J., Delcher, Arthur L., Salzberg, Steven L., Silva, Joana C., Haas, Brian J., Majoros, William H., Farzad, Maryam, Carlton, Jane M., Smith, Robert K. Jr., Garg, Jyoti, Pearlman, Ronald E., Karrer, Kathleen M., Sun, Lei, Manning, Gerard, Elde, Nels C., Turkewitz, Aaron P., Asai, David J., Wilkes, David E., Wang, Yufeng, Cai, Hong, Collins, Kathleen, Stewart, B. Andrew, Lee, Suzanne R., Wilamowsk, Katarzyna, Weinberg, Zasha, Ruzzo, Walter L., Wloga, Dorota, Gaertig, Jacek, Frankel, Joseph, Tsao, Che-Chia, Gorovsky, Martin A., Keeling, Patrick J., Waller, Ross F., Patron, Nicola J., Cherry, J. Michael, Stover, Nicholas A., Krieger, Cynthia J., del Toro, Christina, Ryder, Hilary F., Williamson, Sondra C., Barbeau, Rebecca A., Hamilton, Eileen P., Orias, Eduardo, Eisen, Jonathan A., Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., Badger, Jonathan H., Ren, Qinghu, Amedeo, Paolo, Jones, Kristie M., Tallon, Luke J., Delcher, Arthur L., Salzberg, Steven L., Silva, Joana C., Haas, Brian J., Majoros, William H., Farzad, Maryam, Carlton, Jane M., Smith, Robert K. Jr., Garg, Jyoti, Pearlman, Ronald E., Karrer, Kathleen M., Sun, Lei, Manning, Gerard, Elde, Nels C., Turkewitz, Aaron P., Asai, David J., Wilkes, David E., Wang, Yufeng, Cai, Hong, Collins, Kathleen, Stewart, B. Andrew, Lee, Suzanne R., Wilamowsk, Katarzyna, Weinberg, Zasha, Ruzzo, Walter L., Wloga, Dorota, Gaertig, Jacek, Frankel, Joseph, Tsao, Che-Chia, Gorovsky, Martin A., Keeling, Patrick J., Waller, Ross F., Patron, Nicola J., Cherry, J. Michael, Stover, Nicholas A., Krieger, Cynthia J., del Toro, Christina, Ryder, Hilary F., Williamson, Sondra C., Barbeau, Rebecca A., Hamilton, Eileen P., and Orias, Eduardo

Abstract

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model or

Published
2006

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