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transcriptome evolution

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https://www.readbyqxmd.com/read/28934256/transcriptome-analysis-of-sex-related-genes-in-the-blood-clam-tegillarca-granosa
#1
Heng Chen, Guoqiang Xiao, Xueliang Chai, Xingguan Lin, Jun Fang, Shuangshuang Teng
BACKGROUND: Blood clams (Tegillarca granosa) are one of the most commercial shellfish in China and South Asia with wide distribution in Indo-Pacific tropical to temperate estuaries. However, recent data indicate a decline in the germplasm of this species. Furthermore, the molecular mechanisms underpinning reproductive regulation remain unclear and information regarding genetic diversity is limited. Understanding the reproductive biology of shellfish is important in interpreting their embryology development, reproduction and population structure...
2017: PloS One
https://www.readbyqxmd.com/read/28932623/proteomics-technique-opens-new-frontiers-in-mobilome-research
#2
COMMENT
Andrew D Davidson, David A Matthews, Kevin Maringer
A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the "mobilome," which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the "domestication" of transposon proteins for cellular functions. Although 'omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28928284/functional-and-evolutionary-insights-from-the-ciona-notochord-transcriptome
#3
Wendy M Reeves, Yuye Wu, Matthew J Harder, Michael T Veeman
The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow-sorted notochord cells from multiple stages to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression and extensively validate the results by in situ hybridization. These genes are highly enriched for Gene Ontology terms related to the extracellular matrix, cell adhesion and cytoskeleton...
September 15, 2017: Development
https://www.readbyqxmd.com/read/28927539/transient-and-stable-vector-transfection-pitfalls-off-target-effects-artifacts
#4
REVIEW
Aleksei A Stepanenko, Henry H Heng
Transient and stable vector transfections have played important roles in illustrating the function of specific genes/proteins. The general assumption is that such a platform could effectively link a given gene/protein to gained phenotypes, revealing the mechanism of how a gene works. However, in reality, increased studies have surprisingly noticed some unexpected results. In this review, we demonstrate that an assumption that empty vector-transfected cells preserve the cytogenetic and phenotypic characteristics, and represent the adequate control in transfection experiments is not universally valid...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28927374/b-box-genes-genome-wide-identification-evolution-and-their-contribution-to-pollen-growth-in-pear-pyrus-bretschneideri-rehd
#5
Yunpeng Cao, Yahui Han, Dandan Meng, Dahui Li, Chunyan Jiao, Qing Jin, Yi Lin, Yongping Cai
BACKGROUND: The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in pear. RESULTS: In the present study, a total of 25 BBX genes were identified in pear (Pyrus bretschneideri Rehd.). Subsequently, phylogenetic relationship, gene structure, gene duplication, transcriptome data and qRT-PCR were conducted on these BBX gene members...
September 19, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28924501/identification-and-analysis-of-cyp450-genes-from-transcriptome-of-lonicera-japonica-and-expression-analysis-of-chlorogenic-acid-biosynthesis-related-cyp450s
#6
Xiwu Qi, Xu Yu, Daohua Xu, Hailing Fang, Ke Dong, Weilin Li, Chengyuan Liang
BACKGROUND: Lonicera japonica is an important medicinal plant that has been widely used in traditional Chinese medicine for thousands of years. The pharmacological activities of L. japonica are mainly due to its rich natural active ingredients, most of which are secondary metabolites. CYP450s are a large, complex, and widespread superfamily of proteins that participate in many endogenous and exogenous metabolic reactions, especially secondary metabolism. Here, we identified CYP450s in L...
2017: PeerJ
https://www.readbyqxmd.com/read/28923023/comparative-transcriptomics-of-female-and-male-gametocytes-in-plasmodium-berghei-and-the-evolution-of-sex-in-alveolates
#7
Lee M Yeoh, Christopher D Goodman, Vanessa Mollard, Geoffrey I McFadden, Stuart A Ralph
BACKGROUND: The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into sexual forms, termed gametocytes, which are ingested by a mosquito vector. Sexual differentiation produces either female or male gametocytes, and involves significant morphological and biochemical changes. These transformations prepare gametocytes for the rapid progression to gamete formation and fertilisation, which occur within 20 min of ingestion...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28915794/genome-sequence-of-the-ectophytic-fungus-ramichloridium-luteum-reveals-unique-evolutionary-adaptations-to-plant-surface-niche
#8
Bo Wang, Xiaofei Liang, Mark L Gleason, Rong Zhang, Guangyu Sun
BACKGROUND: Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis. RESULTS: The R...
September 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28902843/the-apostasia-genome-and-the-evolution-of-orchids
#9
Guo-Qiang Zhang, Ke-Wei Liu, Zhen Li, Rolf Lohaus, Yu-Yun Hsiao, Shan-Ce Niu, Jie-Yu Wang, Yao-Cheng Lin, Qing Xu, Li-Jun Chen, Kouki Yoshida, Sumire Fujiwara, Zhi-Wen Wang, Yong-Qiang Zhang, Nobutaka Mitsuda, Meina Wang, Guo-Hui Liu, Lorenzo Pecoraro, Hui-Xia Huang, Xin-Ju Xiao, Min Lin, Xin-Yi Wu, Wan-Lin Wu, You-Yi Chen, Song-Bin Chang, Shingo Sakamoto, Masaru Ohme-Takagi, Masafumi Yagi, Si-Jin Zeng, Ching-Yu Shen, Chuan-Ming Yeh, Yi-Bo Luo, Wen-Chieh Tsai, Yves Van de Peer, Zhong-Jian Liu
Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28900684/transcriptome-changes-in-adaptive-evolution-of-xylose-fermenting-industrial-saccharomyces-cerevisiae-strains-with-%C3%AE-integration-of-different-xyla-genes
#10
Yun-Cheng Li, Wei-Yi Zeng, Min Gou, Zhao-Yong Sun, Zi-Yuan Xia, Yue-Qin Tang
It is of utmost importance to construct industrial xylose-fermenting Saccharomyces cerevisiae strains for lignocellulosic bioethanol production. In this study, two xylose isomerase-based industrial S. cerevisiae strains, O7 and P5, were constructed by δ-integration of the xylose isomerase (XI) gene xylA from the fungus Orpinomyces sp. and from the bacterium Prevotella ruminicola, respectively. The xylose consumption of the strains O7 and P5 at 48-h fermentation was 17.71 and 26.10 g/L, respectively, in synthetic medium with xylose as the sole sugar source...
September 13, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28900436/molecular-resources-from-transcriptomes-in-the-brassicaceae-family
#11
Lua Lopez, Eva M Wolf, J Chris Pires, Patrick P Edger, Marcus A Koch
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28900129/multiple-p450s-and-variation-in-neuronal-genes-underpins-the-response-to-the-insecticide-imidacloprid-in-a-population-of-drosophila-melanogaster
#12
Shane Denecke, Roberto Fusetto, Felipe Martelli, Alex Giang, Paul Battlay, Alexandre Fournier-Level, Richard A O' Hair, Philip Batterham
Insecticide resistance is an economically important example of evolution in response to intense selection pressure. Here, the genetics of resistance to the neonicotinoid insecticide imidacloprid is explored using the Drosophila Genetic Reference Panel, a collection of inbred Drosophila melanogaster genotypes derived from a single population in North Carolina. Imidacloprid resistance varied substantially among genotypes, and more resistant genotypes tended to show increased capacity to metabolize and excrete imidacloprid...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28899718/molecular-characterization-of-circulating-tumor-cells-from-bench-to-bedside
#13
REVIEW
Yanmeng Li, Shaohan Wu, Fan Bai
Circulating tumor cells (CTCs) are cancer cells discovered in cancer patients' peripheral blood that successfully escape from the primary tumor site and/or metastases, struggle to survive in the bloodstream, and have potential for seeding metastases. Numerous methods have been proposed to capture CTCs. The value of CTCs as a means of understanding cancer metastasis and a major form of 'liquid biopsy' has been widely demonstrated. Recently, single-cell molecular analyses of CTCs have provided profound biological insights into tumor heterogeneity, mechanism of metastasis and tumor evolution...
September 9, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28894941/evolutionary-coincidence-of-adaptive-changes-in-exuperantia-and-the-emergence-of-bicoid-in-cyclorrhapha-diptera
#14
Janaina Lima de Oliveira, Iderval Silva Sobrinho-Junior, Samira Chahad-Ehlers, Reinaldo Alves de Brito
The great radiation in the infraorder Cyclorrhapha involved several morphological and molecular changes, including important changes in anterior egg development. During Drosophila oogenesis, exuperantia (exu) is critical for localizing bicoid (bcd) messenger RNA (mRNA) to the anterior region of the oocyte. Because it is phylogenetically older than bcd, which is exclusive to Cyclorrhapha, we hypothesize that exu has undergone adaptive changes to enable this new function. Although exu has been well studied in Drosophila, there is no functional or transcriptional information about it in any other Diptera...
September 11, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28892163/disparity-diversity-and-duplications-in-the-caryophyllales
#15
Stephen A Smith, Joseph W Brown, Ya Yang, Riva Bruenn, Chloe P Drummond, Samuel F Brockington, Joseph F Walker, Noah Last, Norman A Douglas, Michael J Moore
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species...
September 11, 2017: New Phytologist
https://www.readbyqxmd.com/read/28892151/the-genetic-breakdown-of-sporophytic-self-incompatibility-in-tolpis-coronopifolia-asteraceae
#16
Boryana Koseva, Daniel J Crawford, Keely E Brown, Mark E Mort, John K Kelly
Angiosperm diversity has been shaped by mating system evolution, with the most common transition from outcrossing to self-fertilizing. To investigate the genetic basis of this transition, we performed crosses between two species endemic to the Canary Islands, the self-compatible (SC) species Tolpis coronopifolia and its self-incompatible (SI) relative Tolpis santosii. We scored self-compatibility as self-seed set of recombinant plants within two F2 populations. To map and genetically characterize the breakdown of SI, we built a draft genome sequence of T...
September 11, 2017: New Phytologist
https://www.readbyqxmd.com/read/28887149/transcriptome-and-target-dna-enrichment-sequence-data-provide-new-insights-into-the-phylogeny-of-vespid-wasps-hymenoptera-aculeata-vespidae
#17
Sarah Bank, Manuela Sann, Christoph Mayer, Karen Meusemann, Alexander Donath, Lars Podsiadlowski, Alexey Kozlov, Malte Petersen, Lars Krogmann, Rudolf Meier, Paolo Rosa, Thomas Schmitt, Mareike Wurdack, Shanlin Liu, Xin Zhou, Bernhard Misof, Ralph S Peters, Oliver Niehuis
The wasp family Vespidae comprises more than 5000 described species which represent life history strategies ranging from solitary and presocial to eusocial and socially parasitic. The phylogenetic relationships of the major vespid wasp lineages (i.e., subfamilies and tribes) have been investigated repeatedly by analyzing behavioral and morphological traits as well as nucleotide sequences of few selected genes with largely incongruent results. Here we reconstruct their phylogenetic relationships using a phylogenomic approach...
September 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28886704/differentiated-transcriptional-signatures-in-the-maize-landraces-of-chiapas-mexico
#18
Matthew A Kost, Hugo R Perales, Saranga Wijeratne, Asela J Wijeratne, Eric Stockinger, Kristin L Mercer
BACKGROUND: Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. RESULTS: Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico...
September 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28885174/advanced-applications-of-next-generation-sequencing-technologies-to-orchid-biology
#19
Chuan-Ming Yeh, Zhong-Jian Liu, Wen-Chieh Tsai
Next-generation sequencing technologies are revolutionizing biology by permitting, transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide single nucleotide polymorphism profiling. Orchid research has benefited from this breakthrough, and a few orchid genomes are now available; new biological questions can be approached and new breeding strategies can be designed. The first part of this review describes the unique features of orchid biology. The second part provides an overview of the current next-generation sequencing platforms, many of which are already used in plant laboratories...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885172/status-and-prospects-of-next-generation-sequencing-technologies-in-crop-plants
#20
T R Sharma, B N Devanna, Kanti Kiran, Pankaj K Singh, Kirti Arora, Priyanka Jain, Ila M Tiwari, Himanshu Dubey, Banita Saklani, Mandeep Kumari, Jyoti Singh, Rajdeep Jaswal, Ritu Kapoor, Deepak V Pawar, Shruti Sinha, Deepak Singh Bisht, A U Solanke, T K Mondal
The history of DNA sequencing dates back to 1970s. During this period the two first generation nucleotide sequencing techniques were developed. Subsequently the Sanger's dideoxy method of sequencing gained popularity over Maxam and Gilbert's chemical method of sequencing. However, in the last decade, we have observed revolutionary changes in DNA sequencing technologies leading to the emergence of next-generation sequencing (NGS) techniques. NGS technologies have enhanced the throughput and speed of sequencing combined with bringing down the overall cost of the process over a time...
September 8, 2017: Current Issues in Molecular Biology
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