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For: Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, Birren B, Galagan JE, Lander ES. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res 2005;15:1127-35. [PMID: 16077012 PMCID: PMC1182225 DOI: 10.1101/gr.3722605] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Number Cited by Other Article(s)
1
Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. Development 2024;151:dev202968. [PMID: 39114943 PMCID: PMC11441980 DOI: 10.1242/dev.202968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/25/2024] [Indexed: 08/16/2024]
2
Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583753. [PMID: 38559144 PMCID: PMC10979880 DOI: 10.1101/2024.03.06.583753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
3
Puritz JB, Guo X, Hare M, He Y, Hillier LW, Jin S, Liu M, Lotterhos KE, Minx P, Modak T, Proestou D, Rice ES, Tomlinson C, Warren WC, Witkop E, Zhao H, Gomez-Chiarri M. A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference. Mol Ecol Resour 2024;24:e13801. [PMID: 37186213 DOI: 10.1111/1755-0998.13801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
4
Tobias Z, Solow A, Tepolt C. Geography and developmental plasticity shape post-larval thermal tolerance in the golden star tunicate, Botryllus schlosseri. J Therm Biol 2024;119:103763. [PMID: 38071896 DOI: 10.1016/j.jtherbio.2023.103763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 11/19/2023] [Indexed: 02/25/2024]
5
Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023;11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023]  Open
6
Ko BJ, Lee C, Kim J, Rhie A, Yoo DA, Howe K, Wood J, Cho S, Brown S, Formenti G, Jarvis ED, Kim H. Widespread false gene gains caused by duplication errors in genome assemblies. Genome Biol 2022;23:205. [PMID: 36167596 PMCID: PMC9516828 DOI: 10.1186/s13059-022-02764-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/02/2022] [Indexed: 12/22/2022]  Open
7
Stahlke AR, Bitume EV, Özsoy ZA, Bean DW, Veillet A, Clark MI, Clark EI, Moran P, Hufbauer RA, Hohenlohe PA. Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control. Evol Appl 2022;15:60-77. [PMID: 35126648 PMCID: PMC8792477 DOI: 10.1111/eva.13325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/31/2023]  Open
8
Ballarin L, Karahan A, Salvetti A, Rossi L, Manni L, Rinkevich B, Rosner A, Voskoboynik A, Rosental B, Canesi L, Anselmi C, Pinsino A, Tohumcu BE, Jemec Kokalj A, Dolar A, Novak S, Sugni M, Corsi I, Drobne D. Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology. Front Immunol 2021;12:688106. [PMID: 34276677 PMCID: PMC8278520 DOI: 10.3389/fimmu.2021.688106] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]  Open
9
Satou Y, Sato A, Yasuo H, Mihirogi Y, Bishop J, Fujie M, Kawamitsu M, Hisata K, Satoh N. Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages. Genome Biol Evol 2021;13:6209075. [PMID: 33822040 PMCID: PMC8186479 DOI: 10.1093/gbe/evab068] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]  Open
10
Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol 2021;39:309-312. [PMID: 33288905 PMCID: PMC7954703 DOI: 10.1038/s41587-020-0711-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022]
11
Zhao Z, Zhou Y, Wang S, Zhang X, Wang C, Li S. LDscaff: LD-based scaffolding of de novo genome assemblies. BMC Bioinformatics 2020;21:570. [PMID: 33371875 PMCID: PMC7768660 DOI: 10.1186/s12859-020-03895-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022]  Open
12
Cheng YH, Liu CFJ, Yu YH, Jhou YT, Fujishima M, Tsai IJ, Leu JY. Genome plasticity in Paramecium bursaria revealed by population genomics. BMC Biol 2020;18:180. [PMID: 33250052 PMCID: PMC7702705 DOI: 10.1186/s12915-020-00912-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/29/2020] [Indexed: 11/25/2022]  Open
13
A comparative genomics multitool for scientific discovery and conservation. Nature 2020;587:240-245. [PMID: 33177664 PMCID: PMC7759459 DOI: 10.1038/s41586-020-2876-6] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
14
Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res 2020;30:1291-1305. [PMID: 32801147 PMCID: PMC7545148 DOI: 10.1101/gr.263566.120] [Citation(s) in RCA: 420] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
15
Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 2020;9:giaa088. [PMID: 32808665 PMCID: PMC7433188 DOI: 10.1093/gigascience/giaa088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022]  Open
16
DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. Genome Biol Evol 2020;12:948-964. [PMID: 32211845 PMCID: PMC7337526 DOI: 10.1093/gbe/evaa060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 12/21/2022]  Open
17
Norrell AE, Jones KL, Saillant EA. Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis. PLoS One 2020;15:e0232402. [PMID: 32348345 PMCID: PMC7190162 DOI: 10.1371/journal.pone.0232402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022]  Open
18
Sex Chromosome Evolution in Muscid Flies. G3-GENES GENOMES GENETICS 2020;10:1341-1352. [PMID: 32051221 PMCID: PMC7144080 DOI: 10.1534/g3.119.400923] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
19
Qiu B, Fang S, Ikhwanuddin M, Wong L, Ma H. Genome survey and development of polymorphic microsatellite loci for Sillago sihama based on Illumina sequencing technology. Mol Biol Rep 2020;47:3011-3017. [PMID: 32124169 DOI: 10.1007/s11033-020-05348-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
20
Kingan SB, Urban J, Lambert CC, Baybayan P, Childers AK, Coates B, Scheffler B, Hackett K, Korlach J, Geib SM. A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system. Gigascience 2019;8:giz122. [PMID: 31609423 PMCID: PMC6791401 DOI: 10.1093/gigascience/giz122] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]  Open
21
Kuon JE, Qi W, Schläpfer P, Hirsch-Hoffmann M, von Bieberstein PR, Patrignani A, Poveda L, Grob S, Keller M, Shimizu-Inatsugi R, Grossniklaus U, Vanderschuren H, Gruissem W. Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. BMC Biol 2019;17:75. [PMID: 31533702 PMCID: PMC6749633 DOI: 10.1186/s12915-019-0697-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022]  Open
22
Girollet N, Rubio B, Lopez-Roques C, Valière S, Ollat N, Bert PF. De novo phased assembly of the Vitis riparia grape genome. Sci Data 2019;6:127. [PMID: 31324816 PMCID: PMC6642119 DOI: 10.1038/s41597-019-0133-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]  Open
23
A comparative analysis of methods for de novo assembly of hymenopteran genomes using either haploid or diploid samples. Sci Rep 2019;9:6480. [PMID: 31019201 PMCID: PMC6482151 DOI: 10.1038/s41598-019-42795-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/04/2019] [Indexed: 01/05/2023]  Open
24
Ratcliffe LE, Asiedu EK, Pickett CJ, Warburton MA, Izzi SA, Meedel TH. The Ciona myogenic regulatory factor functions as a typical MRF but possesses a novel N-terminus that is essential for activity. Dev Biol 2019;448:210-225. [PMID: 30365920 PMCID: PMC6478573 DOI: 10.1016/j.ydbio.2018.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/28/2018] [Accepted: 10/16/2018] [Indexed: 11/26/2022]
25
Initiation of the zygotic genetic program in the ascidian embryo. Semin Cell Dev Biol 2018;84:111-117. [DOI: 10.1016/j.semcdb.2018.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
26
Roach MJ, Schmidt SA, Borneman AR. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics 2018;19:460. [PMID: 30497373 PMCID: PMC6267036 DOI: 10.1186/s12859-018-2485-7] [Citation(s) in RCA: 663] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/12/2018] [Indexed: 12/04/2022]  Open
27
Roach MJ, Johnson DL, Bohlmann J, van Vuuren HJJ, Jones SJM, Pretorius IS, Schmidt SA, Borneman AR. Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS Genet 2018;14:e1007807. [PMID: 30458008 PMCID: PMC6279053 DOI: 10.1371/journal.pgen.1007807] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/04/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023]  Open
28
Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM. De novo assembly of haplotype-resolved genomes with trio binning. Nat Biotechnol 2018;36:nbt.4277. [PMID: 30346939 PMCID: PMC6476705 DOI: 10.1038/nbt.4277] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 09/10/2018] [Indexed: 12/20/2022]
29
Huang X, Li S, Gao Y, Zhan A. Genome-Wide Identification, Characterization and Expression Analyses of Heat Shock Protein-Related Genes in a Highly Invasive Ascidian Ciona savignyi. Front Physiol 2018;9:1043. [PMID: 30108524 PMCID: PMC6079275 DOI: 10.3389/fphys.2018.01043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/13/2018] [Indexed: 12/02/2022]  Open
30
Satou Y, Imai KS. Ascidian Zic Genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018;1046:87-106. [PMID: 29442319 DOI: 10.1007/978-981-10-7311-3_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
31
Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T. A graph-based approach to diploid genome assembly. Bioinformatics 2018;34:i105-i114. [PMID: 29949989 PMCID: PMC6022571 DOI: 10.1093/bioinformatics/bty279] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
32
Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ. De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Sci Rep 2018;8:5518. [PMID: 29615780 PMCID: PMC5882950 DOI: 10.1038/s41598-018-23749-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 01/17/2023]  Open
33
Shimai K, Kusakabe TG. The Use of cis-Regulatory DNAs as Molecular Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [DOI: 10.1007/978-981-10-7545-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
34
Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation. ADVANCES IN PARASITOLOGY 2018;100:155-208. [PMID: 29753338 DOI: 10.1016/bs.apar.2018.03.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
35
Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms. Trends Genet 2017;34:121-132. [PMID: 29198378 DOI: 10.1016/j.tig.2017.11.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023]
36
Huang X, Li S, Ni P, Gao Y, Jiang B, Zhou Z, Zhan A. Rapid response to changing environments during biological invasions: DNA methylation perspectives. Mol Ecol 2017;26:6621-6633. [PMID: 29057612 DOI: 10.1111/mec.14382] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 10/01/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
37
Tigano A, Sackton TB, Friesen VL. Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia). Mol Ecol Resour 2017;18:79-90. [PMID: 28815912 DOI: 10.1111/1755-0998.12712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
38
Huang S, Kang M, Xu A. HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics 2017;33:2577-2579. [PMID: 28407147 PMCID: PMC5870766 DOI: 10.1093/bioinformatics/btx220] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/31/2017] [Accepted: 04/11/2017] [Indexed: 11/12/2022]  Open
39
Wang K, Dantec C, Lemaire P, Onuma TA, Nishida H. Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi. BMC Genomics 2017;18:314. [PMID: 28427349 PMCID: PMC5399378 DOI: 10.1186/s12864-017-3707-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/12/2017] [Indexed: 11/10/2022]  Open
40
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 2017;356:92-95. [PMID: 28336562 PMCID: PMC5635820 DOI: 10.1126/science.aal3327] [Citation(s) in RCA: 1640] [Impact Index Per Article: 205.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/13/2017] [Indexed: 01/04/2023]
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Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res 2017;27:824-834. [PMID: 28298430 PMCID: PMC5411777 DOI: 10.1101/gr.213959.116] [Citation(s) in RCA: 2480] [Impact Index Per Article: 310.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/13/2017] [Indexed: 01/25/2023]
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Epigenetic divergence of key genes associated with water temperature and salinity in a highly invasive model ascidian. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1409-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
43
Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, Nederbragt AJ. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 2017;18:95. [PMID: 28100185 PMCID: PMC5241972 DOI: 10.1186/s12864-016-3448-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023]  Open
44
Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O’Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 2016;13:1050-1054. [PMID: 27749838 PMCID: PMC5503144 DOI: 10.1038/nmeth.4035] [Citation(s) in RCA: 1286] [Impact Index Per Article: 142.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/25/2016] [Indexed: 02/06/2023]
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Andere AA, Platt RN, Ray DA, Picard CJ. Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research. BMC Genomics 2016;17:842. [PMID: 27793085 PMCID: PMC5084420 DOI: 10.1186/s12864-016-3187-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/22/2016] [Indexed: 01/07/2023]  Open
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Ciona as a Simple Chordate Model for Heart Development and Regeneration. J Cardiovasc Dev Dis 2016;3. [PMID: 27642586 PMCID: PMC5023151 DOI: 10.3390/jcdd3030025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
47
Lemaire P, Piette J. Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley. Open Biol 2016;5:150053. [PMID: 26085517 PMCID: PMC4632506 DOI: 10.1098/rsob.150053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
48
Krehenwinkel H, Rödder D, Tautz D. Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture. GLOBAL CHANGE BIOLOGY 2015;21:4320-32. [PMID: 26183328 DOI: 10.1111/gcb.13042] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/05/2015] [Accepted: 07/01/2015] [Indexed: 05/28/2023]
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Huang X, Gao Y, Jiang B, Zhou Z, Zhan A. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi. Gene 2015;576:79-87. [PMID: 26428313 DOI: 10.1016/j.gene.2015.09.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/16/2015] [Accepted: 09/25/2015] [Indexed: 12/20/2022]
50
Cameron RA, Kudtarkar P, Gordon SM, Worley KC, Gibbs RA. Do echinoderm genomes measure up? Mar Genomics 2015;22:1-9. [PMID: 25701080 PMCID: PMC4489978 DOI: 10.1016/j.margen.2015.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 11/19/2022]
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