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For: Salmela L, Rivals E. LoRDEC: accurate and efficient long read error correction. ACTA ACUST UNITED AC 2014;30:3506-14. [PMID: 25165095 PMCID: PMC4253826 DOI: 10.1093/bioinformatics/btu538] [Citation(s) in RCA: 476] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
251
Peng Z, He Y, Parajuli S, You Q, Wang W, Bhattarai K, Palmateer AJ, Deng Z. Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens. HORTICULTURE RESEARCH 2021;8:108. [PMID: 33931631 PMCID: PMC8087834 DOI: 10.1038/s41438-021-00543-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 05/11/2023]
252
Yang C, Li X, Wang Q, Yuan H, Huang Y, Xiao H. Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications. BMC Genomics 2021;22:311. [PMID: 33926388 PMCID: PMC8082828 DOI: 10.1186/s12864-021-07616-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/14/2021] [Indexed: 12/20/2022]  Open
253
Ramberg S, Høyheim B, Østbye TKK, Andreassen R. A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon. Front Genet 2021;12:656334. [PMID: 33986770 PMCID: PMC8110904 DOI: 10.3389/fgene.2021.656334] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022]  Open
254
Kolchanova S, Komissarov A, Kliver S, Mazo-Vargas A, Afanador Y, Velez-Valentín J, de la Rosa RV, Castro-Marquez S, Rivera-Colon I, Majeske AJ, Wolfsberger WW, Hains T, Corvelo A, Martinez-Cruzado JC, Glenn TC, Robinson O, Koepfli KP, Oleksyk TK. Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles. Genes (Basel) 2021;12:608. [PMID: 33924228 PMCID: PMC8074781 DOI: 10.3390/genes12040608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 01/10/2023]  Open
255
Jiao X, Shi J, Qin S, Huang D, Wang Y. Dataset of the transcriptomes of Urechis unicinctus to identify differentially expressed genes (DEGs) under different temperature and exposure to open air. Data Brief 2021;35:106941. [PMID: 33842678 PMCID: PMC8020418 DOI: 10.1016/j.dib.2021.106941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 10/29/2022]  Open
256
Fernandez‐Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner‐Metzger G, Rensing SA. Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021;106:275-293. [PMID: 33453123 PMCID: PMC8641386 DOI: 10.1111/tpj.15161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 05/06/2023]
257
Panthee S, Paudel A, Hamamoto H, Ogasawara AA, Iwasa T, Blom J, Sekimizu K. Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium. Genomics 2021;113:1534-1542. [PMID: 33771633 DOI: 10.1016/j.ygeno.2021.03.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/10/2021] [Accepted: 03/21/2021] [Indexed: 12/22/2022]
258
Rajewski A, Carter-House D, Stajich J, Litt A. Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture. BMC Genomics 2021;22:201. [PMID: 33752605 PMCID: PMC7986286 DOI: 10.1186/s12864-021-07489-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/26/2021] [Indexed: 11/29/2022]  Open
259
Heo Y, Manikandan G, Ramachandran A, Chen D. Comprehensive Evaluation of Error-Correction Methodologies for Genome Sequencing Data. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
260
Hou Z, Shi F, Ge S, Tao J, Ren L, Wu H, Zong S. Comparative transcriptome analysis of the newly discovered insect vector of the pine wood nematode in China, revealing putative genes related to host plant adaptation. BMC Genomics 2021;22:189. [PMID: 33726671 PMCID: PMC7968331 DOI: 10.1186/s12864-021-07498-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/02/2021] [Indexed: 02/06/2023]  Open
261
Park T, Wijeratne S, Meulia T, Firkins JL, Yu Z. The macronuclear genome of anaerobic ciliate Entodinium caudatum reveals its biological features adapted to the distinct rumen environment. Genomics 2021;113:1416-1427. [PMID: 33722656 DOI: 10.1016/j.ygeno.2021.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/02/2021] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
262
Broseus L, Thomas A, Oldfield AJ, Severac D, Dubois E, Ritchie W. TALC: Transcript-level Aware Long-read Correction. Bioinformatics 2021;36:5000-5006. [PMID: 32910174 DOI: 10.1093/bioinformatics/btaa634] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/08/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]  Open
263
Chen X, Tong C, Zhang X, Song A, Hu M, Dong W, Chen F, Wang Y, Tu J, Liu S, Tang H, Zhang L. A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. PLANT BIOTECHNOLOGY JOURNAL 2021;19:615-630. [PMID: 33073445 PMCID: PMC7955885 DOI: 10.1111/pbi.13493] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 05/03/2023]
264
Liu T, Li M, Liu Z, Ai X, Li Y. Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. HORTICULTURE RESEARCH 2021;8:41. [PMID: 33642572 PMCID: PMC7917095 DOI: 10.1038/s41438-021-00476-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 05/04/2023]
265
Pei T, Yan M, Kong Y, Fan H, Liu J, Cui M, Fang Y, Ge B, Yang J, Zhao Q. The genome of Tripterygium wilfordii and characterization of the celastrol biosynthesis pathway. GIGABYTE 2021;2021:gigabyte14. [PMID: 36967728 PMCID: PMC10038137 DOI: 10.46471/gigabyte.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/25/2021] [Indexed: 11/09/2022]  Open
266
Yang M, Shang X, Zhou Y, Wang C, Wei G, Tang J, Zhang M, Liu Y, Cao J, Zhang Q. Full-Length Transcriptome Analysis of Plasmodium falciparum by Single-Molecule Long-Read Sequencing. Front Cell Infect Microbiol 2021;11:631545. [PMID: 33708645 PMCID: PMC7942025 DOI: 10.3389/fcimb.2021.631545] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/05/2021] [Indexed: 11/25/2022]  Open
267
Li HD, Zhang W, Luo Y, Wang J. IsoDetect: Detection of Splice Isoforms from Third Generation Long Reads Based on Short Feature Sequences. Curr Bioinform 2021. [DOI: 10.2174/1574893615666200316101205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
268
Chen Y, Wan S, Li Q, Dong X, Diao J, Liao Q, Wang GY, Gao ZX. Genome-Wide Integrated Analysis Revealed Functions of lncRNA-miRNA-mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala. Front Cell Dev Biol 2021;8:603815. [PMID: 33614620 PMCID: PMC7891300 DOI: 10.3389/fcell.2020.603815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022]  Open
269
Biological computation and computational biology: survey, challenges, and discussion. Artif Intell Rev 2021. [DOI: 10.1007/s10462-020-09951-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
270
Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis. Mol Cell Biol 2021;41:MCB.00472-20. [PMID: 33168698 DOI: 10.1128/mcb.00472-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022]  Open
271
Rautiainen M, Marschall T. MBG: Minimizer-based Sparse de Bruijn Graph Construction. Bioinformatics 2021;37:2476-2478. [PMID: 33475133 PMCID: PMC8521641 DOI: 10.1093/bioinformatics/btab004] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/14/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]  Open
272
Gan W, Chung-Davidson YW, Chen Z, Song S, Cui W, He W, Zhang Q, Li W, Li M, Ren J. Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish. Sci Rep 2021;11:1815. [PMID: 33469041 PMCID: PMC7815744 DOI: 10.1038/s41598-020-80168-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]  Open
273
Jin S, Bian C, Jiang S, Han K, Xiong Y, Zhang W, Shi C, Qiao H, Gao Z, Li R, Huang Y, Gong Y, You X, Fan G, Shi Q, Fu H. A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense. Gigascience 2021;10:giaa160. [PMID: 33459341 PMCID: PMC7812440 DOI: 10.1093/gigascience/giaa160] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/01/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022]  Open
274
He Z, Su Y, Wang T. Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri. Int J Mol Sci 2021;22:ijms22020787. [PMID: 33466772 PMCID: PMC7830723 DOI: 10.3390/ijms22020787] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/30/2020] [Accepted: 01/02/2021] [Indexed: 02/07/2023]  Open
275
Liu X, Li X, Wen X, Zhang Y, Ding Y, Zhang Y, Gao B, Zhang D. PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response. BMC Genomics 2021;22:52. [PMID: 33446096 PMCID: PMC7809858 DOI: 10.1186/s12864-021-07366-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 01/01/2021] [Indexed: 01/30/2023]  Open
276
Du H, Diao C, Zhao P, Zhou L, Liu JF. Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads. Brief Bioinform 2021;22:6082823. [PMID: 33429431 DOI: 10.1093/bib/bbaa399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 11/12/2022]  Open
277
Morisse P, Marchet C, Limasset A, Lecroq T, Lefebvre A. Scalable long read self-correction and assembly polishing with multiple sequence alignment. Sci Rep 2021;11:761. [PMID: 33436980 PMCID: PMC7804095 DOI: 10.1038/s41598-020-80757-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/22/2020] [Indexed: 11/09/2022]  Open
278
Holley G, Beyter D, Ingimundardottir H, Møller PL, Kristmundsdottir S, Eggertsson HP, Halldorsson BV. Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly. Genome Biol 2021;22:28. [PMID: 33419473 PMCID: PMC7792008 DOI: 10.1186/s13059-020-02244-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022]  Open
279
Tu Z, Shen Y, Wen S, Liu H, Wei L, Li H. A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2021;12:705321. [PMID: 34367224 PMCID: PMC8343429 DOI: 10.3389/fpls.2021.705321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/28/2021] [Indexed: 05/08/2023]
280
Xiong Y, Yu Q, Xiong Y, Zhao J, Lei X, Liu L, Liu W, Peng Y, Zhang J, Li D, Bai S, Ma X. The Complete Mitogenome of Elymus sibiricus and Insights Into Its Evolutionary Pattern Based on Simple Repeat Sequences of Seed Plant Mitogenomes. FRONTIERS IN PLANT SCIENCE 2021;12:802321. [PMID: 35154192 PMCID: PMC8826237 DOI: 10.3389/fpls.2021.802321] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/27/2021] [Indexed: 05/11/2023]
281
Firtina C, Kim JS, Alser M, Senol Cali D, Cicek AE, Alkan C, Mutlu O. Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinformatics 2020;36:3669-3679. [PMID: 32167530 DOI: 10.1093/bioinformatics/btaa179] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 12/16/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022]  Open
282
Zhang H, Jain C, Aluru S. A comprehensive evaluation of long read error correction methods. BMC Genomics 2020;21:889. [PMID: 33349243 PMCID: PMC7751105 DOI: 10.1186/s12864-020-07227-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023]  Open
283
Xu D, Yang H, Zhuo Z, Lu B, Hu J, Yang F. Characterization and analysis of the transcriptome in Opisina arenosella from different developmental stages using single-molecule real-time transcript sequencing and RNA-seq. Int J Biol Macromol 2020;169:216-227. [PMID: 33340629 DOI: 10.1016/j.ijbiomac.2020.12.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/10/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023]
284
Draft Genome of the Common Snapping Turtle, Chelydra serpentina, a Model for Phenotypic Plasticity in Reptiles. G3-GENES GENOMES GENETICS 2020;10:4299-4314. [PMID: 32998935 PMCID: PMC7718744 DOI: 10.1534/g3.120.401440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
285
Zhou SY, Dong QL, Zhu KS, Gao L, Chen X, Xiang H. Long-read transcriptomic analysis of orb-weaving spider Araneus ventricosus indicates transcriptional diversity of spidroins. Int J Biol Macromol 2020;168:395-402. [PMID: 33275979 DOI: 10.1016/j.ijbiomac.2020.11.182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 08/31/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022]
286
Steyaert A, Audenaert P, Fostier J. Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields. BMC Bioinformatics 2020;21:402. [PMID: 32928110 PMCID: PMC7491180 DOI: 10.1186/s12859-020-03740-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/04/2020] [Indexed: 12/01/2022]  Open
287
Deng N, Hou C, He B, Ma F, Song Q, Shi S, Liu C, Tian Y. A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense. BMC PLANT BIOLOGY 2020;20:531. [PMID: 33228526 PMCID: PMC7685604 DOI: 10.1186/s12870-020-02729-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/31/2020] [Indexed: 05/07/2023]
288
Liu J, Wang J, Xiao X, Lai X, Dai D, Zhang X, Zhu X, Zhao Z, Wang J, Li Z. A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model. BMC Genomics 2020;21:753. [PMID: 33208104 PMCID: PMC7677778 DOI: 10.1186/s12864-020-07008-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]  Open
289
Zhang S, Liu Q, Lyu C, Chen J, Xiao R, Chen J, Yang Y, Zhang H, Hou K, Wu W. Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana. BMC Genomics 2020;21:794. [PMID: 33187479 PMCID: PMC7664074 DOI: 10.1186/s12864-020-07195-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/27/2020] [Indexed: 01/21/2023]  Open
290
Yang H, Xu D, Zhuo Z, Hu J, Lu B. Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages. PeerJ 2020;8:e10223. [PMID: 33194414 PMCID: PMC7643551 DOI: 10.7717/peerj.10223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/29/2020] [Indexed: 01/15/2023]  Open
291
Zheng J, Wang P, Mao Y, Su Y, Wang J. Full-length transcriptome analysis provides new insights into the innate immune system of Marsupenaeus japonicus. FISH & SHELLFISH IMMUNOLOGY 2020;106:283-295. [PMID: 32755684 DOI: 10.1016/j.fsi.2020.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
292
Kuo RI, Cheng Y, Zhang R, Brown JWS, Smith J, Archibald AL, Burt DW. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics 2020;21:751. [PMID: 33126848 PMCID: PMC7596999 DOI: 10.1186/s12864-020-07123-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022]  Open
293
The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. PLoS One 2020;15:e0240935. [PMID: 33119641 PMCID: PMC7595290 DOI: 10.1371/journal.pone.0240935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]  Open
294
Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States. mSphere 2020;5:5/5/e00990-20. [PMID: 33115839 PMCID: PMC8534314 DOI: 10.1128/msphere.00990-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
295
Grabski DF, Broseus L, Kumari B, Rekosh D, Hammarskjold ML, Ritchie W. Intron retention and its impact on gene expression and protein diversity: A review and a practical guide. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020;12:e1631. [PMID: 33073477 DOI: 10.1002/wrna.1631] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/16/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
296
Li L, Liu H, Wen W, Huang C, Li X, Xiao S, Wu M, Shi J, Xu D. Full Transcriptome Analysis of Callus Suspension Culture System of Bletilla striata. Front Genet 2020;11:995. [PMID: 33193583 PMCID: PMC7593603 DOI: 10.3389/fgene.2020.00995] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022]  Open
297
Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741). G3-GENES GENOMES GENETICS 2020;10:3497-3504. [PMID: 32747341 PMCID: PMC7534425 DOI: 10.1534/g3.120.401326] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
298
Chen D, Du Y, Fan X, Zhu Z, Jiang H, Wang J, Fan Y, Chen H, Zhou D, Xiong C, Zheng Y, Xu X, Luo Q, Guo R. Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome utilizing PacBio long reads combined with Illumina short reads. J Invertebr Pathol 2020;176:107475. [PMID: 32976816 DOI: 10.1016/j.jip.2020.107475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023]
299
Rautiainen M, Marschall T. GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol 2020;21:253. [PMID: 32972461 PMCID: PMC7513500 DOI: 10.1186/s13059-020-02157-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 08/26/2020] [Indexed: 02/07/2023]  Open
300
Full-length transcriptome sequencing combined with RNA-seq analysis revealed the immune response of fat greenling (Hexagrammos otakii) to Vibrio harveyi in early infection. Microb Pathog 2020;149:104527. [PMID: 32980468 DOI: 10.1016/j.micpath.2020.104527] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 01/20/2023]
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