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https://www.readbyqxmd.com/read/28813471/mitochondrial-genome-evolution-in-the-saccharomyces-sensu-stricto-complex
#1
Jiangxing Ruan, Jian Cheng, Tongcun Zhang, Huifeng Jiang
Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#2
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families)...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812732/genome-of-the-pitcher-plant-cephalotus-reveals-genetic-changes-associated-with-carnivory
#3
Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberly M Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F Shibata, Shuji Shigenobu, Naomi Sumikawa, Taketoshi Uzawa, Meiying Xie, Chunfang Zheng, David D Pollock, Victor A Albert, Shuaicheng Li, Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption...
February 6, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812723/the-unconstrained-evolution-of-fast-and-efficient-antibiotic-resistant-bacterial-genomes
#4
Carlos Reding-Roman, Mark Hewlett, Sarah Duxbury, Fabio Gori, Ivana Gudelj, Robert Beardmore
Evolutionary trajectories are constrained by trade-offs when mutations that benefit one life history trait incur fitness costs in other traits. As resistance to tetracycline antibiotics by increased efflux can be associated with an increase in length of the Escherichia coli chromosome of 10% or more, we sought costs of resistance associated with doxycycline. However, it was difficult to identify any because the growth rate (r), carrying capacity (K) and drug efflux rate of E. coli increased during evolutionary experiments where the species was exposed to doxycycline...
January 30, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812710/developmental-constraints-shape-the-evolution-of-the-nematode-mid-developmental-transition
#5
Harel Zalts, Itai Yanai
Evolutionary theory assumes that genetic variation is uniform and gradual in nature, yet morphological and gene expression studies have revealed that different life-stages exhibit distinct levels of cross-species conservation. In particular, a stage in mid-embryogenesis is highly conserved across species of the same phylum, suggesting that this stage is subject to developmental constraints, either by increased purifying selection or by a strong mutational bias. An alternative explanation, however, holds that the same 'hourglass' pattern of variation may result from increased positive selection at the earlier and later stages of development...
March 27, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812685/scallop-genome-provides-insights-into-evolution-of-bilaterian-karyotype-and-development
#6
Shi Wang, Jinbo Zhang, Wenqian Jiao, Ji Li, Xiaogang Xun, Yan Sun, Ximing Guo, Pin Huan, Bo Dong, Lingling Zhang, Xiaoli Hu, Xiaoqing Sun, Jing Wang, Chengtian Zhao, Yangfan Wang, Dawei Wang, Xiaoting Huang, Ruijia Wang, Jia Lv, Yuli Li, Zhifeng Zhang, Baozhong Liu, Wei Lu, Yuanyuan Hui, Jun Liang, Zunchun Zhou, Rui Hou, Xue Li, Yunchao Liu, Hengde Li, Xianhui Ning, Yu Lin, Liang Zhao, Qiang Xing, Jinzhuang Dou, Yangping Li, Junxia Mao, Haobing Guo, Huaiqian Dou, Tianqi Li, Chuang Mu, Wenkai Jiang, Qiang Fu, Xiaoteng Fu, Yan Miao, Jian Liu, Qian Yu, Ruojiao Li, Huan Liao, Xuan Li, Yifan Kong, Zhi Jiang, Daniel Chourrout, Ruiqiang Li, Zhenmin Bao
Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor...
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812684/genome-evolution-shellfish-genes
#7
Kenneth M Halanych, Kevin M Kocot
No abstract text is available yet for this article.
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812631/contrasting-effects-of-environment-and-genetics-generate-a-continuum-of-parallel-evolution
#8
Yoel E Stuart, Thor Veen, Jesse N Weber, Dieta Hanson, Mark Ravinet, Brian K Lohman, Cole J Thompson, Tania Tasneem, Andrew Doggett, Rebecca Izen, Newaz Ahmed, Rowan D H Barrett, Andrew P Hendry, Catherine L Peichel, Daniel I Bolnick
Parallel evolution of similar traits by independent populations in similar environments is considered strong evidence for adaptation by natural selection. Often, however, replicate populations in similar environments do not all evolve in the same way, thus deviating from any single, predominant outcome of evolution. This variation might arise from non-adaptive, population-specific effects of genetic drift, gene flow or limited genetic variation. Alternatively, these deviations from parallel evolution might also reflect predictable adaptation to cryptic environmental heterogeneity within discrete habitat categories...
May 22, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812563/multicopy-plasmids-potentiate-the-evolution-of-antibiotic-resistance-in-bacteria
#9
Alvaro San Millan, Jose Antonio Escudero, Danna R Gifford, Didier Mazel, R Craig MacLean
Plasmids are thought to play a key role in bacterial evolution by acting as vehicles for horizontal gene transfer, but the role of plasmids as catalysts of gene evolution remains unexplored. We challenged populations of Escherichia coli carrying the blaTEM-1 β-lactamase gene on either the chromosome or a multicopy plasmid (19 copies per cell) with increasing concentrations of ceftazidime. The plasmid accelerated resistance evolution by increasing the rate of appearance of novel TEM-1 mutations, thereby conferring resistance to ceftazidime, and then by amplifying the effect of TEM-1 mutations due to the increased gene dosage...
November 7, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812460/myopathic-mtdna-depletion-syndrome-due-to-mutation-in-tk2-gene
#10
Elena Martín-Hernández, María Teresa García-Silva, Pilar Quijada-Fraile, María Elena Rodríguez-García, Henry Rivera, Aurelio Hernández-Laín, David Coca-Robinot, Joaquín Fernández-Toral, Joaquín Arenas, Miguel A Martín, Francisco Martínez-Azorín
Whole-exome sequencing was used to identify the disease gene(s) in a Spanish girl with failure to thrive, muscle weakness, mild facial weakness, elevated creatine kinase, deficiency of mitochondrial complex III and depletion of mtDNA. With whole-exome sequencing data, it was possible to get the whole mtDNA sequencing and discard any pathogenic variant in this genome. The analysis of whole exome uncovered a homozygous pathogenic mutation in thymidine kinase 2 gene ( TK2; NM_004614.4:c.323 C>T, p.T108M)...
September 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28811619/comparative-mitogenomic-analysis-of-aposthonia-borneensis-and-aposthonia-japonica-embioptera-oligotomidae-reveals-divergent-evolution-of-webspinners
#11
Zhi-Teng Chen, Liang Lü, Ming-Xing Lu, Yu-Zhou Du
In this study, we report the complete mitochondrial genome (mitogenome, mtDNA) of Aposthonia borneensis and compare it with another sequenced webspinner, Aposthonia japonica. The A. borneensis mitogenome is smaller than A. japonica, but the size of each gene and the A + T content of protein-coding genes (PCGs) are almost identical in the two mitogenomes. Among the PCGs, atp6 shows the highest evolutionary rate and cox1 the lowest. The mtDNA map in A. borneensis is similar to Drosophila yakuba, but distinctly different from A...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811564/computational-identification-of-y-linked-markers-and-genes-in-the-grass-carp-genome-by-using-a-pool-and-sequence-method
#12
Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zuoyan Zhu, Yaping Wang
The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811498/genome-re-sequencing-reveals-the-history-of-apple-and-supports-a-two-stage-model-for-fruit-enlargement
#13
Naibin Duan, Yang Bai, Honghe Sun, Nan Wang, Yumin Ma, Mingjun Li, Xin Wang, Chen Jiao, Noah Legall, Linyong Mao, Sibao Wan, Kun Wang, Tianming He, Shouqian Feng, Zongying Zhang, Zhiquan Mao, Xiang Shen, Xiaoliu Chen, Yuanmao Jiang, Shujing Wu, Chengmiao Yin, Shunfeng Ge, Long Yang, Shenghui Jiang, Haifeng Xu, Jingxuan Liu, Deyun Wang, Changzhi Qu, Yicheng Wang, Weifang Zuo, Li Xiang, Chang Liu, Daoyuan Zhang, Yuan Gao, Yimin Xu, Kenong Xu, Thomas Chao, Gennaro Fazio, Huairui Shu, Gan-Yuan Zhong, Lailiang Cheng, Zhangjun Fei, Xuesen Chen
Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811388/hill-robertson-interference-reduces-genetic-diversity-on-a-young-plant-y-chromosome
#14
Josh Hough, Wei Wang, Spencer C H Barrett, Stephen I Wright
X and Y chromosomes differ in effective population size (Ne ), rates of recombination, and exposure to natural selection, all of which can affect patterns of genetic diversity. On Y chromosomes with suppressed recombination, natural selection is expected to eliminate linked neutral variation and lower the Ne of Y compared to X chromosomes or autosomes. However, female-biased sex ratios and high variance in male reproductive success can also reduce Y-linked Ne , making it difficult to infer the causes of low Y-diversity...
August 15, 2017: Genetics
https://www.readbyqxmd.com/read/28811374/recruitment-of-crispr-cas-systems-by-tn7-like-transposons
#15
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28811342/bacteriophages-of-gordonia-spp-display-a-spectrum-of-diversity-and-genetic-relationships
#16
Welkin H Pope, Travis N Mavrich, Rebecca A Garlena, Carlos A Guerrero-Bustamante, Deborah Jacobs-Sera, Matthew T Montgomery, Daniel A Russell, Marcie H Warner, Graham F Hatfull
The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are "singletons" with no closely related genomes...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28811313/a-key-role-for-foxq2-in-anterior-head-and-central-brain-patterning-in-insects
#17
Peter Kitzmann, Matthias Weißkopf, Magdalena Ines Schacht, Gregor Bucher
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the red flour beetle Tribolium castaneum ortholog of foxQ2 (Tc-foxQ2) as a novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression...
August 15, 2017: Development
https://www.readbyqxmd.com/read/28811072/evolution-of-hemoglobin-loci-and-their-regulatory-elements
#18
REVIEW
Sjaak Philipsen, Ross C Hardison
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene...
August 9, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/28810920/erratum-to-genomic-innovations-transcriptional-plasticity-and-gene-loss-underlying-the-evolution-and-divergence-of-two-highly-polyphagous-and-invasive-helicoverpa-pest-species
#19
S L Pearce, D F Clarke, P D East, S Elfekih, K H J Gordon, L S Jermiin, A McGaughran, J G Oakeshott, A Papanicolaou, O P Perera, R V Rane, S Richards, W T Tay, T K Walsh, A Anderson, C J Anderson, S Asgari, P G Board, A Bretschneider, P M Campbell, T Chertemps, J T Christeller, C W Coppin, S J Downes, G Duan, C A Farnsworth, R T Good, L B Han, Y C Han, K Hatje, I Horne, Y P Huang, D S T Hughes, E Jacquin-Joly, W James, S Jhangiani, M Kollmar, S S Kuwar, S Li, N-Y Liu, M T Maibeche, J R Miller, N Montagne, T Perry, J Qu, S V Song, G G Sutton, H Vogel, B P Walenz, W Xu, H-J Zhang, Z Zou, P Batterham, O R Edwards, R Feyereisen, R A Gibbs, D G Heckel, A McGrath, C Robin, S E Scherer, K C Worley, Y D Wu
No abstract text is available yet for this article.
August 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28810712/genomic-analysis-of-the-evolution-of-phototrophy-among-haloalkaliphilic-rhodobacterales
#20
Karel Kopejtka, Jürgen Tomasch, Yonghui Zeng, Martin Tichý, Dimitry Y Sorokin, Michal Koblížek
A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans...
July 1, 2017: Genome Biology and Evolution
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