1
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Estupiñán RA, Torres de Farias S, Gonçalves EC, Camargo M, Cruz Schneider MP. Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae). Zookeys 2023; 1149:145-169. [DOI: 10.3897/zookeys.1149.85627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/22/2022] [Indexed: 02/24/2023] Open
Abstract
Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories.
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2
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Molecular tools for resolving Merodon ruficornis group (Diptera, Syrphidae) taxonomy. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00571-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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3
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Boutte J, Fishbein M, Straub SCK. NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data. Methods Mol Biol 2022; 2512:61-72. [PMID: 35817999 DOI: 10.1007/978-1-0716-2429-6_4] [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] [Indexed: 06/15/2023]
Abstract
Hypothesized evolutionary insertions and deletions in nucleic acid sequences (indels) contain significant phylogenetic information and can be integrated in phylogenomic analyses. However, assemblies of short reads obtained from next-generation sequencing (NGS) technologies can contain errors that result in falsely inferred indels that need to be detected and omitted to avoid inclusion in phylogenetic analysis. Here, we detail the commands that comprise a new version of the NGS-Indel Coder pipeline, which was developed to validate indels using assembly read depth.
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Affiliation(s)
- Julien Boutte
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA.
| | - Mark Fishbein
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA
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4
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Ren T, Zhang Z, Fu R, Yang Y, Li W, Liang J, Mo G, Luo W, Zhang X. A 51 bp indel polymorphism within the PTH1R gene is significantly associated with chicken growth and carcass traits. Anim Genet 2020; 51:568-578. [PMID: 32400914 DOI: 10.1111/age.12942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2020] [Indexed: 01/04/2023]
Abstract
Parathyroid hormone (PTH) is a crucial regulator of calcium homeostasis and bone remodeling, and the parathyroid hormone 1 receptor (PTH1R) belongs to a class II G-protein-coupled receptor. PTH activates PTH1R, which mediates catabolic and anabolic processes in the skeleton. However, the functional mechanism of PTH1R has not been thoroughly elucidated in organisms. This study identified a 51 bp indel mutation in the first intron of the PTH1R gene and elucidated the effect of this gene mutation on the growth and carcass traits in chickens. The results indicated that the 51 bp indel was significantly associated with subcutaneous fat thickness, abdominal fat weight, body weight and daily gain over 4-8 weeks. Furthermore, we found that PTH1R gene expression was highest in the kidney and liver tissues, and it showed a trend of decreasing in leg and breast muscle tissues at different embryonic stages. In addition, we examined the expression of the three genotypes of the PTH1R gene in the liver, breast muscle and abdominal fat and found that the II genotype was significantly higher than the DD and ID genotypes. In summary, these findings suggest that the PTH1R gene can serve as a potential molecular marker for chicken breeding.
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Affiliation(s)
- T Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Z Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - R Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Y Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - W Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - J Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - G Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - W Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - X Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
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5
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Liang K, Wang X, Tian X, Geng R, Li W, Jing Z, Han R, Tian Y, Liu X, Kang X, Li Z. Molecular characterization and an 80-bp indel polymorphism within the prolactin receptor ( PRLR) gene and its associations with chicken growth and carcass traits. 3 Biotech 2019; 9:296. [PMID: 31321200 DOI: 10.1007/s13205-019-1827-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/07/2019] [Indexed: 01/09/2023] Open
Abstract
The prolactin receptor (PRLR), a type I cytokine receptor, must bind prolactin (PRL) to act on target cells to mediate various physiological functions, including reproduction and lactation. This study identified an 80-bp insertion/deletion (indel) polymorphism in the 3'-untranslated region (3'-UTR) of the chicken PRLR gene in 3736 individuals from 15 breeds and analyzed its associations with growth and carcass traits in an F2 resource population. The results of the association analysis indicated that the 80-bp indel polymorphism was significantly (P < 0.05) or very significantly (P < 0.01) associated with multiple growth and carcass traits, such as body weight, leg weight, and shank length. In addition, we found that during the breeding process of commercial laying hens and commercial broilers, the 80-bp indel locus was artificially selected for the II genotype. Together, our findings reveal that this 80-bp indel polymorphism has potential as a new molecular marker for marker-assisted selection of chicken growth and carcass traits.
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Affiliation(s)
- Ke Liang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaoxiao Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Rui Geng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Wenya Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Zhenzhu Jing
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
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Abstract
The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves.
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Boutte J, Fishbein M, Liston A, Straub SCK. NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias). Mol Phylogenet Evol 2019; 139:106534. [PMID: 31212081 DOI: 10.1016/j.ympev.2019.106534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/12/2019] [Accepted: 06/13/2019] [Indexed: 12/30/2022]
Abstract
Targeted genome sequencing approaches allow characterization of evolutionary relationships using a considerable number of nuclear genes and informative characters. However, most phylogenomic analyses only utilize single nucleotide polymorphisms (SNPs). Studies at the species level, especially in groups that have recently radiated, often recover low amounts of phylogenetically informative variation in coding regions, and require non-coding sequences, which are richer in indels, to resolve gene trees. Here, NGS-Indel Coder, a pipeline to detect and omit false positive indels inferred from assemblies of short read sequence data, was developed to resolve the relationships among and within major clades of the American milkweeds (Asclepias), which are the result of a rapid and recent evolutionary radiation, and whose phylogeny has been difficult to resolve. This pipeline was applied to a Hyb-Seq data set of 768 loci including targeted exons and flanking intron regions from 33 milkweed species. Robust species tree inference was improved by excluding small alignment partitions (<100 bp) that increased gene tree ambiguity and incongruence. To further investigate the robustness of indel coding, data sets that included small and large indels were explored, and species trees derived from concatenated loci versus coalescent methods based on gene trees were compared. The phylogeny of Asclepias obtained using nuclear data was well resolved, and phylogenetic information from indels improved resolution of specific nodes. The Temperate North American, Mexican Highland, and Incarnatae clades were well supported as monophyletic. Asclepias coulteri, which has been considered part of the Sonoran Desert clade based on plastome analyses, was placed as sister to all the other milkweed species studied here, rather than as a member of that clade. Two groups within the Temperate North American and Mexican clades were not resolved, and the inferred relationships strongly conflicted when comparing results based on data sets that did or did not include indel characters. This new pipeline represents a step forward in making maximal use of the information content in phylogenomic data sets.
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Affiliation(s)
- Julien Boutte
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA
| | - Mark Fishbein
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA.
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8
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Donath A, Stadler PF. Split-inducing indels in phylogenomic analysis. Algorithms Mol Biol 2018; 13:12. [PMID: 30026791 PMCID: PMC6047143 DOI: 10.1186/s13015-018-0130-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 06/16/2018] [Indexed: 11/13/2022] Open
Abstract
Background Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps. Results Here we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (splids) that define an approximate bipartition of the taxon set. We show both in simulated data and in case studies on real-life data that splids can be efficiently extracted from phylogenomic data sets. Conclusions Suitably processed gap patterns extracted from genome-wide alignment provide a surprisingly clear phylogenetic signal and an allow the inference of accurate phylogenetic trees. Electronic supplementary material The online version of this article (10.1186/s13015-018-0130-7) contains supplementary material, which is available to authorized users.
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9
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Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
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10
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Drake I, White Jr JF, Belanger FC. Identification of the fungal endophyte of Ammophila breviligulata (American beachgrass) as Epichloë amarillans. PeerJ 2018; 6:e4300. [PMID: 29375938 PMCID: PMC5784578 DOI: 10.7717/peerj.4300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/08/2018] [Indexed: 11/20/2022] Open
Abstract
The grass Ammophila breviligulata (American beachgrass) is known to host an endophyte of the genus Epichloë. Based on morphological characteristics it was originally identified as Acremonium typhinum var. ammophilae and is currently designated as Epichloë typhina var. ammophilae. However, the Epichloë species has not previously been identified based on DNA sequence data. Based on phylogenetic placement of beta-tubulin and translation elongation factor 1-alpha DNA sequences the endophyte is identified as a member of E. amarillans rather than E. typhina.
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Affiliation(s)
- Ian Drake
- Department of Biology, William Paterson University, Wayne, NJ, United States of America
| | - James F. White Jr
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
| | - Faith C. Belanger
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
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11
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Hasegawa M, Kuroda S. Phylogeny mandalas of birds using the lithographs of John Gould’s folio bird books. Mol Phylogenet Evol 2017; 117:141-149. [DOI: 10.1016/j.ympev.2016.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022]
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12
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Malone CL, Reynoso VH, Buckley L. Never judge an iguana by its spines: Systematics of the Yucatan spiny tailed iguana, Ctenosaura defensor (Cope, 1866). Mol Phylogenet Evol 2017; 115:27-39. [PMID: 28716742 DOI: 10.1016/j.ympev.2017.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 06/13/2017] [Accepted: 07/13/2017] [Indexed: 01/05/2023]
Abstract
Spiny tailed iguanas are highly diverse clade of lizards in Mesoamerica, ranging from northern Mexico through Panama. Utilizing 2 regions of mitochondrial DNA (1948bp) and 4 nuclear loci (2232bp) we explored the relationships between these species and the phylogeographic history of the major clades. We discovered that the lineage endemic to the Yucatan Peninsula renders the genus Ctenosaura paraphyletic. To resolve this non-monophyly, we resurrect the taxon Cachryx Cope, 1866, and provide a new diagnosis for the genus. We also find that small body-size and highly spinose tails in the species previously referred to the subgenus Enyaliosaurus, have evolved independently 3 times. Cachryx were recovered as sister to the lineage of iguanines endemic to the Galapagos Islands, and we discuss biogeographic scenarios to explain this relationship as well as those among the primary clades of Ctenosaura in Mesoamerica.
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Affiliation(s)
- Catherine L Malone
- Department of Biology, Utah Valley University, Orem, UT 84058, United States.
| | - Víctor Hugo Reynoso
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México C.P. 04510, Mexico.
| | - Larry Buckley
- Thomas H. Gosnell School of Science and Math, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, United States.
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13
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Dyomin AG, Koshel EI, Kiselev AM, Saifitdinova AF, Galkina SA, Fukagawa T, Kostareva AA, Gaginskaya ER. Chicken rRNA Gene Cluster Structure. PLoS One 2016; 11:e0157464. [PMID: 27299357 PMCID: PMC4907446 DOI: 10.1371/journal.pone.0157464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/31/2016] [Indexed: 11/18/2022] Open
Abstract
Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5'ETS (1836 bp), 18S rRNA gene (1823 bp), ITS1 (2530 bp), 5.8S rRNA gene (157 bp), ITS2 (733 bp), 28S rRNA gene (4441 bp) and 3'ETS (343 bp). The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region). The results have confirmed the chicken rRNA gene cluster validity.
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Affiliation(s)
| | - Elena I. Koshel
- Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Artem M. Kiselev
- Almazov Federal Medical Research Centre, Saint Petersburg, 197341, Russia
- ITMO University, Saint Petersburg, 197101, Russia
| | | | | | | | - Anna A. Kostareva
- Almazov Federal Medical Research Centre, Saint Petersburg, 197341, Russia
- ITMO University, Saint Petersburg, 197101, Russia
| | - Elena R. Gaginskaya
- Saint Petersburg State University, Saint Petersburg, 199034, Russia
- * E-mail:
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14
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Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. BIOLOGY 2013; 2:419-44. [PMID: 24832669 PMCID: PMC4009869 DOI: 10.3390/biology2010419] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
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Affiliation(s)
- Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - John Harshman
- 4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Jena L. Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
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15
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McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One 2013; 8:e54848. [PMID: 23382987 PMCID: PMC3558522 DOI: 10.1371/journal.pone.0054848] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.
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Affiliation(s)
- John E McCormack
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA.
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Denton JS, Wheeler WC. Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis. Cladistics 2012; 28:514-528. [DOI: 10.1111/j.1096-0031.2012.00402.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Taxonomic placement of Epichloë poae sp. nov. and horizontal dissemination to seedlings via conidia. FUNGAL DIVERS 2012. [DOI: 10.1007/s13225-012-0170-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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