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1. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

Author:
Demircioğlu, Deniz; Cukuroglu, Engin; Kindermans, Martin; Nandi, Tannistha; Calabrese, Claudia; Fonseca, Nuno A.; Kahles, André; Lehmann, Kjong-Van; Stegle, Oliver; Brazma, Alvis; Brooks, Angela N.; Rätsch, Gunnar; Tan, Patrick; Göke, Jonathan
Source:
Cell 2019 v.178 no.6 pp. 1465-1477.e17
ISSN:
0092-8674
Subject:
transcriptome,   etc   ; gene expression; genes; global change; landscapes; neoplasms; patients; sequence analysis; tissues; transcription (genetics); transcriptomics;     Show all 11 Subjects
Abstract:
... Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of transcriptional activity. However, while a global change in transcription is recognized as a defining feature of cancer, the contribution of alternative promoters still remains largely unexplored. Here, we infer active promoters using RNA-seq data fr ...
DOI:
10.1016/j.cell.2019.08.018

2. Transcriptome and QTL analyses reveal candidate genes for fiber quality in Upland cotton

Author:
Wang, Hantao; Zhang, Ruiting; Shen, Chao; Li, Ximei; Zhu, De; Lin, Zhongxu
Source:
The crop journal 2019
ISSN:
2214-5141
Subject:
transcriptome,   etc   ; Gossypium hirsutum; data collection; gene expression regulation; genes; lint cotton; micronaire; parents; pistil; quantitative trait loci; sequence analysis; tissues;     Show all 12 Subjects
Abstract:
... With increasing demand for high-quality cotton, it is desirable to identify genes involved in fiber development for molecular improvement of cotton. In this study, 780 differentially expressed genes (DEGs) were identified in developing fibers at 10 days post-anthesis (DPA) in Gossypium hirsutum acc. DH962 and G. hirsutum cv. Jimian 5 using RNA-seq. Of 15 stable QTL for fiber quality identified in ...
DOI:
10.1016/j.cj.2019.05.002

3. Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

Author:
Gong, Li; Fan, Guangyi; Ren, Yandong; Chen, Yongjiu; Qiu, Qiang; Liu, Liqin; Qin, Yanli; Liu, Bingjian; Jiang, Lihua; Li, Haorong; Zeng, Yan; Gao, Qionghua; Zhang, Chen; Wang, Zhongkai; Jiang, Hui; Tian, Jinfu; Zhang, He; Liu, Xin; Xu, Xun; Wang, Wen; Lü, Zhenming; Li, Yongxin
Source:
Molecular ecology resources 2019 v.19 no.3 pp. 744-756
ISSN:
1755-098X
Subject:
transcriptome,   etc   ; Tachypleus tridentatus; arthropods; blood cells; chromosomes; coagulation; ecosystems; enzyme activity; evolution; genes; genomics; immunity; signal transduction; tissues;     Show all 14 Subjects
Abstract:
... Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods and living fossil species which have existed on the earth for ~500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome‐level T. tridentatus genome, and proved that this genome is of high quality with contig N50 1.69 Mb. By ...
DOI:
10.1111/1755-0998.12988

4. Symposium review: Omics in dairy and animal science—Promise, potential, and pitfalls

Author:
Lippolis, J.D.; Powell, E.J.; Reinhardt, T.A.; Thacker, T.C.; Casas, E.
Source:
Journal of dairy science 2019 v.102 no.5 pp. 4741-4754
ISSN:
0022-0302
Subject:
transcriptome,   etc   ; algorithms; animal health; animals; computers; data collection; databases; genes; instrumentation; messenger RNA; prediction; proteome; proteomics; tissues; transcriptomics;     Show all 15 Subjects
Abstract:
... Sequencing the first genome took 15 yr and $3 billion to complete. Currently, a genome can be sequenced in a day for a few thousand dollars. Comparing the relative abundance of nearly every mRNA transcript and small RNAs from cells and tissues from different experimental conditions has become so easy that it can take longer to transfer the data between computers than to perform the experiment. Nuc ...
DOI:
10.3168/jds.2018-15267

5. Carbohydrate metabolism and fertility related genes high expression levels promote heterosis in autotetraploid rice harboring double neutral genes

Author:
Chen, Lin; Yuan, Yun; Wu, Jinwen; Chen, Zhixiong; Wang, Lan; Shahid, Muhammad Qasim; Liu, Xiangdong
Source:
Rice 2019 v.12 no.1 pp. 34
ISSN:
1939-8425
Subject:
transcriptome,   etc   ; abortion (plants); autotetraploidy; carbohydrate metabolism; chromosomes; flowering; gene expression regulation; genes; heterosis; hybrids; leaves; meiosis; parents; pollen; quantitative trait loci; rice; seed set; starch synthase; tissues; transcriptomics;     Show all 20 Subjects
Abstract:
... BACKGROUND: Autotetraploid rice hybrids have great potential to increase the production, but hybrid sterility is a major hindrance in the utilization of hybrid vigor in polyploid rice, which is mainly caused by pollen abortion. Our previous study showed that double pollen fertility neutral genes, Sa-n and Sb-n, can overcome hybrid sterility in autotetraploid rice. Here, we used an autotetraploid r ...
DOI:
10.1186/s12284-019-0294-x

6. Differential color development and response to light deprivation of fig (Ficus carica L.) syconia peel and female flower tissues: transcriptome elucidation

Author:
Wang, Ziran; Song, Miaoyu; Li, Yunze; Chen, Shangwu; Ma, Huiqin
Source:
BMC plant biology 2019 v.19 no.1 pp. 217
ISSN:
1471-2229
Subject:
transcriptome,   etc   ; Ficus carica; anthocyanins; color; consumer preferences; cyanidin; female flowers; figs; fruit quality; fruits; gene expression regulation; genes; pigmentation; promoter regions; ripening; sequence analysis; tissues; transcription factors; yeasts;     Show all 19 Subjects
Abstract:
... BACKGROUND: Color directly affects fruit quality and consumer preference. In fig syconia, the female flower tissue is contained in a receptacle. Anthocyanin pigmentation of this tissue and the peel differs temporally and spatially. A transcriptome study was carried out to elucidate key genes and transcription factors regulating differences in fig coloring. RESULTS: Anthocyanins in the female flowe ...
DOI:
10.1186/s12870-019-1816-9

7. Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor

Author:
Honaas, Loren A.; Jones, Sam; Farrell, Nina; Kamerow, William; Zhang, Huiting; Vescio, Kathryn; Altman, Naomi S.; Yoder, John I.; dePamphilis, Claude W.
Source:
BMC plant biology 2019 v.19 no.1 pp. 334
ISSN:
1471-2229
Subject:
transcriptome,   etc   ; Angiospermae; data collection; genes; germination; haustoria; host plants; host-parasite relationships; mortality; nutrients; parasitic plants; parasitism; phenotype; plant physiology; stress response; tissues;     Show all 16 Subjects
Abstract:
... BACKGROUND: Parasitic plants engage in a complex molecular dialog with potential host plants to identify a host and overcome host defenses to initiate development of the parasitic feeding organ, the haustorium, invade host tissues, and withdraw water and nutrients. While one of two critical signaling events in the parasitic plant life cycle (germination via stimulant chemicals) has been relatively ...
DOI:
10.1186/s12870-019-1856-1

8. Transcriptome analysis of ovary in relatively greater and lesser egg producing Jinghai Yellow Chicken

Author:
Zhang, Tao; Chen, Lan; Han, Kunpeng; Zhang, Xiangqian; Zhang, Genxi; Dai, Guojun; Wang, Jinyu; Xie, Kaizhou
Source:
Animal reproduction science 2019 v.208 pp. 106114
ISSN:
0378-4320
Subject:
transcriptome,   etc   ; calcium signaling; egg production; eggs; focal adhesions; gene expression; gene expression regulation; gene ontology; genes; hens; messenger RNA; sequence analysis; tissues; transcriptomics;     Show all 14 Subjects
Abstract:
... Egg production is determined by the function of ovary and is regulated by the hypothalamic-pituitary-ovary axis. The mechanism by which the ovary regulates egg production, however, is still poorly understood. The purpose of this study is to compare the transcriptome difference in ovary of relatively greater and lesser egg producing chickens, and to screen candidate genes related to egg production. ...
DOI:
10.1016/j.anireprosci.2019.106114

9. Transcriptome-based Discovery of AP2/ERF tRanscription Factors and Expression Profiles Under Herbivore Stress Conditions in Bamboo (Bambusa emeiensis)

Author:
Li, Yuanqiu; Luo, Chaobing; Chen, Ying; Xiao, Ximeng; Fu, Chun; Yang, Yaojun
Source:
Journal of plant biology 2019 v.62 no.4 pp. 297-306
ISSN:
1226-9239
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; Bambusa emeiensis; amino acids; bamboos; ethylene; gene expression regulation; genes; phylogeny; phytophagous insects; quantitative polymerase chain reaction; tissues; transcription factors;     Show all 13 Subjects
Abstract:
... Bambusa emeiensis is one of the most economically important bamboos, yet the yield and quality of this bamboo species continue to be challenged by insect herbivores. APETALA2/ethylene responsive factors (AP2/ERF) comprise a large family of plant transcription factors regulating numerous biological processes and playing critical roles in plant defence responses. In the present study, 47 AP2/ERF gen ...
DOI:
10.1007/s12374-019-0059-5

10. Close encounters between Trypanosoma cruzi and the host mammalian cell: Lessons from genome-wide expression studies

Author:
Oliveira, Antonio Edson R.; Grazielle-Silva, Viviane; Ferreira, Ludmila R.P.; Teixeira, Santuza M.R.
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
transcriptome,   etc   ; Chagas disease; Trypanosoma cruzi; animal models; biomarkers; disease progression; energy metabolism; etiological agents; genes; immune response; mammals; microarray technology; parasites; pathogenesis; patients; sequence analysis; tissues;     Show all 17 Subjects
Abstract:
... Trypanosoma cruzi is the etiologic agent of Chagas disease, a life-threatening disease that affects different tissues. Within its mammalian host, T. cruzi develops molecular strategies for successful invasion of different cell types and adaptation to the intracellular environment. Conversely, the host cell responds to the infection by activating intracellular pathways to control parasite replicati ...
DOI:
10.1016/j.ygeno.2019.06.015

11. Comparative studies on duplicated tdrd7 paralogs in teleosts: Molecular evolution caused neo-functionalization

Author:
Wang, Bo; Du, Xinxin; Wang, Huizhen; Jin, Chaofan; Gao, Chen; Liu, Jinxiang; Zhang, Quanqi
Source:
Comparative biochemistry and physiology 2019 v.30 pp. 347-357
ISSN:
1744-117X
Subject:
transcriptome,   etc   ; 3' untranslated regions; Danio rerio; Lepisosteus oculatus; Paralichthys olivaceus; adults; bioinformatics; embryo (animal); flounder; genes; genomics; germ cells; gonads; mammals; phylogeny; proteins; tissues;     Show all 17 Subjects
Abstract:
... The third-round whole genome duplication (3R-WGD) event occurred in the stem lineage of teleost during evolution, and is considered to be responsible for the biological diversification of ray-finned fishes. TUDOR domain containing protein 7 (Tdrd7), which belongs to the Tudor family proteins has been widely discussed in mammals. However, information about this gene in teleost is still lacking. In ...
DOI:
10.1016/j.cbd.2019.04.006

12. De novo assembly, characterization of tissue-specific transcriptomes and identification of immune related genes from the scallop Argopecten purpuratus

Author:
Flores-Herrera, Patricio; Farlora, Rodolfo; González, Roxana; Brokordt, Katherina; Schmitt, Paulina
Source:
Fish & shellfish immunology 2019 v.89 pp. 505-515
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Argopecten purpuratus; cDNA libraries; complementary DNA; gene expression regulation; gene ontology; genes; gills; hemocytes; high-throughput nucleotide sequencing; immune response; mortality; mucosal immunity; scallops; shellfish; tissues;     Show all 16 Subjects
Abstract:
... The scallop Argopecten purpuratus is one of the most economically important cultured mollusks on the coasts from Chile and Peru but its production has declined, in part, due to the emergence of mass mortality events of unknown origin. Driven by this scenario, increasing progress has been made in recent years in the comprehension of immune response mechanisms in this species. However, it is still n ...
DOI:
10.1016/j.fsi.2019.03.069

13. Transcriptional analysis of a delayed-flowering mutant under short-day conditions reveal genes related to photoperiodic response in tossa jute (Corchorus olitorius L.)

Author:
Choudhary, Shashi Bhushan; Saha, Dipnarayan; Sharma, Hariom Kumar; Chowdhury, Isholeena; Kumar, A. Anil; Jambhulkar, Sanjay Kumar; Mitra, Jivan
Source:
Industrial crops and products 2019 v.132 pp. 476-486
ISSN:
0926-6690
Subject:
transcriptome,   etc   ; Corchorus olitorius; cultivars; databases; flowering; gene editing; gene expression; gene expression regulation; genes; genetic improvement; jute; leaves; messenger RNA; mutants; proteins; sequence analysis; tissues; transcription (genetics);     Show all 18 Subjects
Abstract:
... Photoperiod profoundly determines reproductive and vegetative development in jute which is extremely correlated to fibre yield and quality. Yet, our understanding of how the photoperiodic genes regulate vegetative and reproductive growth in jute remain unresolved. We developed RNA-seq data from shoot apex tissues of a delayed-flowering mutant (pfr 59) and its wild-type cultivar JRO-204 grown under ...
DOI:
10.1016/j.indcrop.2019.03.001

14. Co-cultures of Oophila amblystomatis between Ambystoma maculatum and Ambystoma gracile hosts show host-symbiont fidelity

Author:
Kerney, Ryan; Leavitt, Jasper; Hill, Elizabeth; Zhang, Huanjia; Kim, Eunsoo; Burns, John
Source:
Symbiosis 2019 v.78 no.1 pp. 73-85
ISSN:
0334-5114
Subject:
transcriptome,   etc   ; Ambystoma; Oophila; algae; ammonia; carbon metabolism; cell walls; coculture; eggs; gene expression; genes; hosts; mutualism; nitrogen metabolism; photosynthesis; salamanders and newts; tissues;     Show all 17 Subjects
Abstract:
... A unique symbiosis occurs between embryos of the spotted salamander (Ambystoma maculatum) and a green alga (Oophila amblystomatis). Unlike most vertebrate host-symbiont relationships, which are ectosymbiotic, A. maculatum exhibits both an ecto- and an endo-symbiosis, where some of the green algal cells living inside egg capsules enter embryonic tissues as well as individual salamander cells. Past ...
DOI:
10.1007/s13199-018-00591-2

15. Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana

Author:
Liu, Wei; Lin, Liping; Zhang, Zhiyuan; Liu, Siqi; Gao, Kuan; Lv, Yanbin; Tao, Huan; He, Huaqin
Source:
Planta 2019 v.249 no.5 pp. 1487-1501
ISSN:
0032-0935
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; chloroplasts; computer software; gene expression; gene expression regulation; genes; heat shock proteins; microarray technology; models; phenotype; rice; tissues; world wide web;     Show all 14 Subjects
Abstract:
... MAIN CONCLUSION: A comprehensive network of the Arabidopsis transcriptome was analyzed and may serve as a valuable resource for candidate gene function investigations. A web tool to explore module information was also provided. Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substantially profiled in various tissues, development stages and other conditions. These ...
DOI:
10.1007/s00425-019-03102-9

16. Overexpression of BcbZIP134 negatively regulates the biosynthesis of saikosaponins

Author:
Xu, Jiao; Wu, Su-Rui; Xu, Yan-Hong; Ge, Zhan-Yu; Sui, Chun; Wei, Jian-He
Source:
Plant cell, tissue, and organ culture 2019 v.137 no.2 pp. 297-308
ISSN:
0167-6857
Subject:
transcriptome,   etc   ; Bupleurum chinense; adventitious roots; antioxidants; antiviral properties; biosynthesis; flowers; fruits; gene expression regulation; genes; herbal medicines; leaves; tissues; transcription factors; triterpenoid saponins;     Show all 15 Subjects
Abstract:
... Chaihu, the dried roots of several Bupleurum species, are widely used as herbal drugs. Triterpene saponins, as saikosaponins (SSs) in Chaihu, exhibit a wide range of pharmacological actions, including significant anti-inflammatory, immunomodulatory, hepatoprotective, antioxidant, anti-tumor and antiviral activities. To explore the regulatory biosynthesis of SS in Bupleurum chinense roots, we scree ...
DOI:
10.1007/s11240-019-01571-0

17. Pectin induced transcriptome of a Rhizoctonia solani strain causing sheath blight disease in rice reveals insights on key genes and RNAi machinery for development of pathogen derived resistance

Author:
Rao, Talluri Bhaskar; Chopperla, Ramakrishna; Methre, Ramesh; Punniakotti, E.; Venkatesh, V.; Sailaja, B.; Reddy, M. Raghurami; Yugander, Arra; Laha, G. S.; Madhav, M. Sheshu; Sundaram, R. M.; Ladhalakshmi, D.; Balachandran, S. M.; Mangrauthia, Satendra K.
Source:
Plant molecular biology 2019 v.100 no.1-2 pp. 59-71
ISSN:
0167-4412
Subject:
transcriptome,   etc   ; RNA interference; Thanatephorus cucumeris; crop production; cultivars; disease resistance; fungi; fungicides; genes; leaf blight; metabolism; pathogens; pectins; pollution; polygalacturonase; proteins; rice; tissues; transcriptomics; virulent strains;     Show all 20 Subjects
Abstract:
... KEY MESSAGE : RNAi mediated silencing of pectin degrading enzyme of R. solani gives a high level of resistance against sheath blight disease of rice. Rice sheath blight disease caused by Rhizoctonia solani Kuhn (telemorph; Thanatephorus cucumeris) is one of the most devastating fungal diseases which cause severe loss to rice grain production. In the absence of resistant cultivars, the disease is c ...
DOI:
10.1007/s11103-019-00843-9

18. Transcriptomic Analysis of Orange Fruit Treated with Pomegranate Peel Extract (PGE)

Author:
Belgacem, Imen; Pangallo, Sonia; Abdelfattah, Ahmed; Romeo, Flora V.; Cacciola, Santa O.; Li Destri Nicosia, Maria G.; Ballistreri, Gabriele; Schena, Leonardo
Source:
Plants 2019 v.8 no.4
ISSN:
2223-7747
Subject:
transcriptome,   etc   ; antibiotics; antimicrobial properties; biochemical pathways; biosynthesis; fruits; gene expression regulation; gene ontology; genes; host plants; oranges; plant diseases and disorders; pomegranates; sequence analysis; tissues; transcriptomics;     Show all 16 Subjects
Abstract:
... A Pomegranate Peel Extract (PGE) has been proposed as a natural antifungal substance with a wide range of activity against plant diseases. Previous studies showed that the extract has a direct antimicrobial activity and can elicit resistance responses in plant host tissues. In the present study, the transcriptomic response of orange fruit toward PGE treatments was evaluated. RNA-seq analyses, cond ...
DOI:
10.3390/plants8040101

19. De novo assembly of Vriesea carinata leaf transcriptome to identify candidate cysteine-proteases

Author:
Eguiluz, M.; Kulcheski, F.R.; Margis, R.; Guzman, F.
Source:
Gene 2019 v.691 pp. 96-105
ISSN:
0378-1119
Subject:
transcriptome,   etc   ; Vriesea; biochemical pathways; cell differentiation; forests; gene expression regulation; gene ontology; genes; genomics; leaves; legumain; nutrients; programmed cell death; proteins; tissues; transcriptomics; trichomes;     Show all 17 Subjects
Abstract:
... Vriesea carinata is an endemic bromeliad from the Brazilian Atlantic Forest. It has trichome and tank system in their leaves which allows to absorb water and nutrients. It belongs to Bromeliaceae family, which includes several species highly enriched of cysteine-proteases (CysPs). These proteolytic enzymes regulate processes as senescence, cell differentiation, pathogen-linked programmed cell deat ...
DOI:
10.1016/j.gene.2018.12.053

20. Comparative Transcriptome Analysis Reveals a More Complicated Adipogenic Process in Intramuscular Stem Cells than That of Subcutaneous Vascular Stem Cells

Author:
Chen, Luxi; Zhang, Yue; Chen, Hu; Zhang, Xumeng; Liu, Xiaohong; He, Zuyong; Cong, Peiqing; Chen, Yaosheng; Mo, Delin
Source:
Journal of agricultural and food chemistry 2019 v.67 no.16 pp. 4700-4708
ISSN:
1520-5118
Subject:
transcriptome,   etc   ; adipocytes; adipogenesis; biosynthesis; gene expression regulation; genes; growth performance; intramuscular fat; pork quality; stem cells; subcutaneous fat; taste; tissues; transcriptomics; unsaturated fatty acids;     Show all 15 Subjects
Abstract:
... Fat-related traits have great influences on pork quality. As different fat tissues have different biochemical profiles depending on their location, intramuscular fat contributes to gustatory qualities, while subcutaneous fat is considered as a negative factor associated with growth performance. In this study, both primary intramuscular and subcutaneous vascular stem cells (IVSCs and SVSCs) could b ...
DOI:
10.1021/acs.jafc.9b00856