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For: Zhou W, Soghigian J, Xiang QYJ. A New Pipeline for Removing Paralogs in Target Enrichment Data. Syst Biol 2021;71:410-425. [PMID: 34146111 PMCID: PMC8974407 DOI: 10.1093/sysbio/syab044] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 06/04/2021] [Accepted: 06/12/2021] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Shazib SUA, Ahsan R, Leleu M, McManus GB, Katz LA, Santoferrara LF. Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing - A case study with planktonic ciliates (Ciliophora, Oligotrichea). Mol Phylogenet Evol 2025;204:108239. [PMID: 39551225 DOI: 10.1016/j.ympev.2024.108239] [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: 07/07/2024] [Revised: 10/25/2024] [Accepted: 11/10/2024] [Indexed: 11/19/2024]
2
Cull A, Joly DL. Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars. BMC Genomics 2025;26:83. [PMID: 39875833 PMCID: PMC11773717 DOI: 10.1186/s12864-025-11263-z] [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: 10/07/2024] [Accepted: 01/20/2025] [Indexed: 01/30/2025]  Open
3
Musker SD, Nürk NM, Pirie MD. Maximising informativeness for target capture-based phylogenomics in Erica (Ericaceae). PHYTOKEYS 2025;251:87-118. [PMID: 39867481 PMCID: PMC11758362 DOI: 10.3897/phytokeys.251.136373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 12/03/2024] [Indexed: 01/28/2025]
4
Ousmael KM, Hansen OK. From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis? APPLICATIONS IN PLANT SCIENCES 2025;13:e11624. [PMID: 39906492 PMCID: PMC11788909 DOI: 10.1002/aps3.11624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 02/06/2025]
5
Shin S, Baker AJ, Enk J, McKenna DD, Foquet B, Vandergast AG, Weissman DB, Song H. Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales. Sci Rep 2024;14:21377. [PMID: 39271747 PMCID: PMC11399444 DOI: 10.1038/s41598-024-72622-6] [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: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024]  Open
6
Ning W, Meudt HM, Tate JA. A roadmap of phylogenomic methods for studying polyploid plant genera. APPLICATIONS IN PLANT SCIENCES 2024;12:e11580. [PMID: 39184196 PMCID: PMC11342234 DOI: 10.1002/aps3.11580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/10/2023] [Accepted: 01/13/2024] [Indexed: 08/27/2024]
7
Xie P, Guo Y, Teng Y, Zhou W, Yu Y. GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data. Mol Ecol Resour 2024;24:e13924. [PMID: 38197287 DOI: 10.1111/1755-0998.13924] [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: 04/16/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/11/2024]
8
Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024;66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
9
Kuo LY, Su HJ, Koubínová D, Xie PJ, Whitehouse C, Ebihara A, Grant JR. Organellar phylogenomics of Ophioglossaceae fern genera. FRONTIERS IN PLANT SCIENCE 2024;14:1294716. [PMID: 38288414 PMCID: PMC10823028 DOI: 10.3389/fpls.2023.1294716] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
10
Moore‐Pollard ER, Jones DS, Mandel JR. Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems. APPLICATIONS IN PLANT SCIENCES 2024;12:e11568. [PMID: 38369976 PMCID: PMC10873820 DOI: 10.1002/aps3.11568] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/30/2023] [Accepted: 11/12/2023] [Indexed: 02/20/2024]
11
Zhou W, Shi W, Soltis PS, Soltis DE, Xiang QY(J. Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation. FRONTIERS IN PLANT SCIENCE 2023;14:1274746. [PMID: 38192694 PMCID: PMC10773735 DOI: 10.3389/fpls.2023.1274746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/27/2023] [Indexed: 01/10/2024]
12
Yang LH, Shi XZ, Wen F, Kang M. Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae). ANNALS OF BOTANY 2023;131:953-966. [PMID: 37177810 PMCID: PMC10332401 DOI: 10.1093/aob/mcad047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023]
13
Gao Y, Zhu J, Zhai H, Xu K, Zhu X, Wu H, Zhang W, Wu S, Chen X, Xia Z. Dysfunction of an Anaphase-Promoting Complex Subunit 8 Homolog Leads to Super-Short Petioles and Enlarged Petiole Angles in Soybean. Int J Mol Sci 2023;24:11024. [PMID: 37446203 DOI: 10.3390/ijms241311024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]  Open
14
Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023;11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
15
Ma’ruf M, Fadli JC, Mahendra MR, Irham LM, Sulistyani N, Adikusuma W, Chong R, Septama AW. A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome. Genomics Inform 2023;21:e26. [PMID: 37704211 PMCID: PMC10326529 DOI: 10.5808/gi.23010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 07/08/2023]  Open
16
Pouchon C, Boluda CG. REFMAKER: make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae. Mol Phylogenet Evol 2023:107826. [PMID: 37257798 DOI: 10.1016/j.ympev.2023.107826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
17
Walden N, Schranz ME. Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae. Genome Biol Evol 2023;15:7059155. [PMID: 36848527 PMCID: PMC10016055 DOI: 10.1093/gbe/evad034] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/27/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023]  Open
18
Omeershffudin UNM, Kumar S. Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics. Genomics Inform 2023;21:e5. [PMID: 37037463 PMCID: PMC10085745 DOI: 10.5808/gi.22066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 04/03/2023]  Open
19
Du ZY, Jenny Xiang QY, Cheng J, Zhou W, Wang QF, Soltis DE, Soltis PS. An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data. AMERICAN JOURNAL OF BOTANY 2023;110:e16116. [PMID: 36480351 DOI: 10.1002/ajb2.16116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
20
Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023;65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
21
Reginato M. A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 2022;10:e14525. [PMID: 36523475 PMCID: PMC9745922 DOI: 10.7717/peerj.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]  Open
22
Zhang Z, Xie P, Guo Y, Zhou W, Liu E, Yu Y. Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research. Mol Biol Evol 2022;39:6862883. [PMID: 36458838 PMCID: PMC9757696 DOI: 10.1093/molbev/msac261] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]  Open
23
Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan. PLoS One 2022;17:e0272680. [PMID: 36178903 PMCID: PMC9524695 DOI: 10.1371/journal.pone.0272680] [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: 07/24/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022]  Open
24
Thureborn O, Razafimandimbison SG, Wikström N, Rydin C. Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae). FRONTIERS IN PLANT SCIENCE 2022;13:967456. [PMID: 36160958 PMCID: PMC9493367 DOI: 10.3389/fpls.2022.967456] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
25
Zhou W, Jenny Xiang QY. Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches. Mol Phylogenet Evol 2022;176:107592. [DOI: 10.1016/j.ympev.2022.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 10/31/2022]
26
Ufimov R, Gorospe JM, Fér T, Kandziora M, Salomon L, van Loo M, Schmickl R. Utilizing paralogs for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data. Mol Ecol Resour 2022;22:3018-3034. [PMID: 35796729 DOI: 10.1111/1755-0998.13684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/28/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022]
27
Pouchon C, Boyer F, Roquet C, Denoeud F, Chave J, Coissac E, Alsos IG, Lavergne S. ORTHOSKIM: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications. Mol Ecol Resour 2022;22:2018-2037. [PMID: 35015377 DOI: 10.1111/1755-0998.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
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