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Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE. Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). PHYTOKEYS 2022; 205:3-58. [PMID: 36762007 PMCID: PMC9848904 DOI: 10.3897/phytokeys.205.85866] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 05/05/2023]
Abstract
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
- Present address: Evolutionary Biology & Ecology, Université Libre de Bruxelles, Faculté des Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt, 50, 1050 Bruxelles, BelgiumUniversité Libre de BruxellesBruxellesBelgium
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, Capão do Leão 96010-900, Rio Grande do Sul, BrazilUniversidade Federal de PelotasRio Grande do SulBrazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, 91501-970, BrazilUniversidade Federal do Rio Grande do SulRio Grande do SulBrazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n – Novo Horizonte, 44036-900, Feira de Santana, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, AustraliaRoyal Botanic Gardens VictoriaMelbourneAustralia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB)ParisFrance
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, CanadaUniversité de MontréalMontrealCanada
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USACornell UniversityIthacaUnited States of America
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UKAccelerated Taxonomy Department, Royal Botanic GardensRichmondUnited Kingdom
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
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2
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Abdel-Hamid AME, Elenazy HH, Abdel-Hameed UK. DNA barcoding of some taxa of genus Acacia and their phylogenetic relationship. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1938702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Amal M. E. Abdel-Hamid
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt
- Department of Biology, College of Sciences and Arts, Taibah University, Al Ula, Kingdom of Saudi Arabia
| | - Hanaa H. Elenazy
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
| | - Usama K. Abdel-Hameed
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
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3
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Chincoya DA, Sanchez-Flores A, Estrada K, Díaz-Velásquez CE, González-Rodríguez A, Vaca-Paniagua F, Dávila P, Arias S, Solórzano S. Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales). Genes (Basel) 2020; 11:E830. [PMID: 32708269 PMCID: PMC7397273 DOI: 10.3390/genes11070830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 01/23/2023] Open
Abstract
In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500-1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.
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Affiliation(s)
- Delil A Chincoya
- Laboratorio de Ecología Molecular y Evolución, Unidad de Biotecnología y Prototipos FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Mexico
| | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, Cuernavaca 62250, Mexico
| | - Karel Estrada
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, Cuernavaca 62250, Mexico
| | - Clara E Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, FES Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Mexico
| | - Antonio González-Rodríguez
- Laboratorio de Genética de la Conservación, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda San José La Huerta, Morelia 58190, Mexico
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, FES Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 04510, Mexico
| | - Patricia Dávila
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos, FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Mexico
| | - Salvador Arias
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
| | - Sofía Solórzano
- Laboratorio de Ecología Molecular y Evolución, Unidad de Biotecnología y Prototipos FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz 54090, Mexico
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Asaf S, Khan A, Khan AL, Al-Harrasi A, Al-Rawahi A. Complete Chloroplast Genomes of Vachellia nilotica and Senegalia senegal: Comparative Genomics and Phylogenomic Placement in a New Generic System. PLoS One 2019; 14:e0225469. [PMID: 31765416 PMCID: PMC6876885 DOI: 10.1371/journal.pone.0225469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022] Open
Abstract
Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica and Senegalia senegal. Therefore, sequencing the chloroplast (cp) genomes of these species and determining their phylogenetic placement via conserved genes may help to validate the taxonomy. Hence, we sequenced the cp genomes of V. nilotica and S. senegal, and the results showed that the sizes of the genomes are 165.3 and 162.7 kb, respectively. The cp genomes of both species comprised large single-copy regions (93,849~91,791 bp) and pairs of inverted repeats (IR; 26,093~26,008 bp). The total numbers of genes found in the V. nilotica and S. senegal cp genomes were 135 and 132, respectively. Approximately 123:130 repeats and 290:281 simple sequence repeats were found in the S. senegal and V. nilotica cp genomes, respectively. Genomic characterization was undertaken by comparing these genomes with those of 17 species belonging to related genera in Fabaceae. A phylogenetic analysis of the whole genome dataset and 56 shared genes was undertaken by generating cladograms with the same topologies and placing both species in a new generic system. These results support the likelihood of identifying segregate genera from Acacia with phylogenomic disposition of both V. nilotica and S. senegal in the subfamily Mimosoideae. The current study is the first to obtain complete genomic information on both species and may help to elucidate the genome architecture of these species and evaluate the genetic diversity among species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Arif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodo, Norway
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- * E-mail: (ALK); (AAH)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- * E-mail: (ALK); (AAH)
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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5
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Khan A, Choudhary G, Ivo T, Jeon H, Benedetti E. Real-Time Intraoperative Assessment of Microcirculation in Living-Donor Small Bowel Transplant: A Case Report. EXP CLIN TRANSPLANT 2019; 19:1110-1113. [PMID: 31324135 DOI: 10.6002/ect.2019.0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Living-donor small bowel transplant has emerged as a modality to transplant patients with short bowel syndrome without prolonged wait time, albeit at the cost of technical challenges associated with vascular anastomosis due to the small size of vessels. Suboptimal perfusion in a transplanted bowel can lead to a devastating outcome, and clinical judgment alone is not completely reliable for assessment of bowel microcirculation. Here, we report a 55-year-old female patient who underwent flow cytometric cross-match-positive living-donor bowel transplant from her daughter. Initial suboptimal perfusion prompted a revision of the arterial anastomoses. Despite normal Doppler signals over the mesenteric vessels, the bowel had a variegated appearance. The microcirculation of the bowel wall was subsequently assessed in a real-time fashion by indocyanine green fluorescence angiography, which showed improved perfusion indices with time. Hence, this simple test helped us to avoid another unnecessary exploration and revision of the anastomoses. At present, the patient is thriving on an enteral diet. This case underpins the importance of real-time intraoperative assessment of bowel per-fusion and microcirculation in difficult cases. These assessments are needed to help surgeons identify tissues at risk for ischemia and necrosis, thereby allowing for maneuvers to improve intestinal viability.
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Affiliation(s)
- Arshad Khan
- From the Division of Transplantation and Division of Surgery, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois, USA.,From the Department of Surgery, Altru Health System, Grand Forks, North Dakota, USA
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6
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Beukes CW, Boshoff FS, Phalane FL, Hassen AI, le Roux MM, Stȩpkowski T, Venter SN, Steenkamp ET. Both Alpha- and Beta-Rhizobia Occupy the Root Nodules of Vachellia karroo in South Africa. Front Microbiol 2019; 10:1195. [PMID: 31214140 PMCID: PMC6558075 DOI: 10.3389/fmicb.2019.01195] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Vachellia karroo (formerly Acacia karroo) is a wide-spread legume species indigenous to southern Africa. Little is known regarding the identity or diversity of rhizobia that associate with this plant in its native range in South Africa. The aims of this study were therefore: (i) to gather a collection of rhizobia associated with V. karroo from a wide range of geographic locations and biomes; (ii) to identify the isolates and infer their evolutionary relationships with known rhizobia; (iii) to confirm their nodulation abilities by using them in inoculation assays to induce nodules under glasshouse conditions. To achieve these aims, soil samples were collected from 28 locations in seven biomes throughout South Africa, which were then used to grow V. karroo seedlings under nitrogen-free conditions. The resulting 88 bacterial isolates were identified to genus-level using 16S rRNA sequence analysis and to putative species-level using recA-based phylogenetic analyses. Our results showed that the rhizobial isolates represented members of several genera of Alphaproteobacteria (Bradyrhizobium, Ensifer, Mesorhizobium, and Rhizobium), as well as Paraburkholderia from the Betaproteobacteria. Our study therefore greatly increases the known number of Paraburkholderia isolates which can associate with this southern African mimosoid host. We also show for the first time that members of this genus can associate with legumes, not only in the Fynbos biome, but also in the Albany Thicket and Succulent Karoo biomes. Twenty-six putative species were delineated among the 88 isolates, many of which appeared to be new to Science with other likely being conspecific or closely related to E. alkalisoli, M. abyssinicae, M. shonense, and P. tropica. We encountered only a single isolate of Bradyrhizobium, which is in contrast to the dominant association of this genus with Australian Acacia. V. karroo also associates with diverse genera in the Grassland biome where it is quite invasive and involved in bush encroachment. Our findings therefore suggest that V. karroo is a promiscuous host capable of forming effective nodules with both alpha- and beta-rhizobia, which could be a driving force behind the ecological success of this tree species.
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Affiliation(s)
- Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Francois S Boshoff
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Francina L Phalane
- Agricultural Research Council, Plant Health and Protection Institute, Pretoria, South Africa
| | - Ahmed I Hassen
- Agricultural Research Council, Plant Health and Protection Institute, Pretoria, South Africa
| | - Marianne M le Roux
- South African National Biodiversity Institute, Pretoria National Botanical Garden, Pretoria, South Africa.,Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | - Tomasz Stȩpkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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Brito AFS, Souza ÉRD, Conceição ADS. The tribes Acacieae and Ingeae (Leguminosae: Caesalpinioideae) in the Environmental Protection Area Serra Branca, Raso da Catarina, Jeremoabo, Bahia, Brazil. BIOTA NEOTROPICA 2019. [DOI: 10.1590/1676-0611-bn-2018-0586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Leguminosae includes six subfamilies, where the traditionally recognised subfamily Mimosoideae was accepted as a distinct clade included within the recircumscribed subfamily Caesalpinioideae, called informally as Mimosoid clade. The representatives of the tribes Acacieae and Ingeae can be differentiated principally in terms of the patterns of their stamens, being free in Acacieae and monadelphous in Ingeae. The floristic survey of Acacieae and Ingeae in the Environmental Protection Area Serra Branca included analysis of specimens collected from June 2011 to September 2012. The analyses were supplemented with dried collections from the following herbaria: ALCB, HRB and HUEFS. Ten species were cataloged, distributed among four genera of Ingeae: Calliandra Benth. (1 sp.), Chloroleucon (Benth.) Britton & Rose ex Record (1 sp.), Enterolobium Mart. (1 sp.), Pithecellobium Mart. (1 sp.); and one genus of Acacieae: Senegalia Raf. (6 spp.). The most representative species were Calliandra aeschynomenoides Benth. associated with sandy and stony soils and Chloroleucon foliolosum (Benth.) G.P.Lewis and Senegalia bahiensis (Benth.) Seigler & Ebinger growing on sandy-clay soils. The taxonomic treatment includes a key for the identification, descriptions, illustrations, photos, data of the geographical distribution phenological data and comments about the species.
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8
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Williams AV, Miller JT, Small I, Nevill PG, Boykin LM. Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia. Mol Phylogenet Evol 2016; 96:1-8. [DOI: 10.1016/j.ympev.2015.11.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
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9
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Talat F, Wang K. Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species. IRANIAN JOURNAL OF BIOTECHNOLOGY 2015; 13:47-56. [PMID: 28959299 DOI: 10.15171/ijb.1231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton.G. thurberi belongs to D genome, which is an important wild bio-source for the cotton breeding and genetic research. To a certain degree, chloroplast DNA sequence information are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. Present study was conducted in order to analyse the sequence of its chloroplast. OBJECTIVES Present study was conducted to study and compare the complete chloroplast sequence of G. thurberi, analyses of its genome structure, gene content and organization, repeat sequence and codon usage and comparison with two cultivated allotetraploid sequenced cotton species. MATERIALS AND METHODS The available sequence was assembled by DNAman (Version 8.1.2.378). Gene annotation was mainly performed by DOGMA. The map of genome structure and gene distribution were carried out using OGDRAW V1.1. Relative synonymous codon usage (RSCU) of different codons in each gene sample was calculated by codonW in Mobyle. To determine the repeat sequence and location, an online version of REPuter was used. RESULTS The G. thurberi chloroplast (cp) genome is 160264 bp in length with conserved quadripartite structure. Single copy region of cp genome is separated by the two inverted regions. The large single copy region is 88,737 bp, and the small single copy region is 20,271 bp whereas the inverted repeat is 25,628 bp each. The plastidic genome has 113 single genes and 20 duplicated genes. The singletones encode 79 proteins, 4 ribosomal RNA genes and 30 transfer RNA genes. CONCLUSIONS Amongst all plastidic genes only 18 genes appeared to have 1-2 introns and when compared with cpDNA of two cultivated allotetraploid, rps18 was the only duplicated gene in G.thurberi. Despite the high level of conservation in cp genome SSRs ,these are useful in analysis of genetic diversity due to their greater efficiency as opposed to genomic SSRs. Low GC content is a significant feature of plastidic genomes, which is possibly formed after endosymbiosis by DNA replication and repair.
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Affiliation(s)
- Farshid Talat
- West Azerbaijan Agricultural and Natural Resources Research Center, AREEO, Urmia, Iran.,Cotton Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China
| | - Kunbo Wang
- Cotton Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, Henan, China
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Steven G N, Subramanyam R. Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Mol Ecol Resour 2013; 9 Suppl s1:172-80. [PMID: 21564976 DOI: 10.1111/j.1755-0998.2009.02642.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acacia species are quite difficult to differentiate using morphological characters. Routine identification of Acacia samples is important in order to distinguish invasive species from rare species or those of economic importance, particularly in the forest industry. The genus Acacia is quite abundant and diverse comprising approximately 1355 species, which is currently divided into three subgenera: subg. Acacia (c. 161 species), subg. Aculiferum (c. 235 species), and subg. Phyllodineae (c. 960 species). It would be prudent to utilize DNA barcoding in the accurate and efficient identification of acacias. The objective of this research is to test barcoding in discriminating multiple populations among a sister-species complex in pantropical Acacia subg. Acacia, across three continents. Based on previous research, we chose three cpDNA regions (rbcL, trnH-psbA and matK). Our results show that all three regions (rbcL, matK and trnH-psbA) can distinguish and support the newly proposed genera of Vachellia Wight & Arn. from Acacia Mill., discriminate sister species within either genera and differentiate biogeographical patterns among populations from India, Africa and Australia. A morphometric analysis confirmed the cryptic nature of these sister species and the limitations of a classification based on phenetic data. These results support the claim that DNA barcoding is a powerful tool for taxonomy and biogeography with utility for identifying cryptic species, biogeograhic patterns and resolving classifications at the rank of genera and species.
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Affiliation(s)
- Newmaster Steven G
- Floristic Diversity Research Group, Biodiversity Institute of Ontario Herbarium (OAC), University of Guelph, Guelph, Ontario, Canada N1G 2W1
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11
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Miller JT, Murphy DJ, Brown GK, Richardson DM, González-Orozco CE. The evolution and phylogenetic placement of invasive Australian Acacia species. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00780.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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12
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Gómez-Acevedo S, Rico-Arce L, Delgado-Salinas A, Magallón S, Eguiarte LE. Neotropical mutualism between Acacia and Pseudomyrmex: Phylogeny and divergence times. Mol Phylogenet Evol 2010; 56:393-408. [DOI: 10.1016/j.ympev.2010.03.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 03/04/2010] [Accepted: 03/15/2010] [Indexed: 11/24/2022]
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13
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Kato T, Bonet A, Yoshitake H, Romero-Nápoles J, Jinbo U, Ito M, Shimada M. Evolution of host utilization patterns in the seed beetle genus Mimosestes Bridwell (Coleoptera: Chrysomelidae: Bruchinae). Mol Phylogenet Evol 2010; 55:816-32. [DOI: 10.1016/j.ympev.2010.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 02/26/2010] [Accepted: 03/01/2010] [Indexed: 11/16/2022]
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14
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Kergoat GJ, Silvain JF, Buranapanichpan S, Tuda M. When insects help to resolve plant phylogeny: evidence for a paraphyletic genus Acacia from the systematics and host-plant range of their seed-predators. ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2006.00266.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Heil M, Greiner S, Meimberg H, Krüger R, Noyer JL, Heubl G, Linsenmair KE, Boland W. Evolutionary change from induced to constitutive expression of an indirect plant resistance. Nature 2004; 430:205-8. [PMID: 15241414 DOI: 10.1038/nature02703] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Accepted: 05/21/2004] [Indexed: 11/08/2022]
Abstract
Induced plant resistance traits are expressed in response to attack and occur throughout the plant kingdom. Despite their general occurrence, the evolution of such resistances has rarely been investigated. Here we report that extrafloral nectar, a usually inducible trait, is constitutively secreted by Central American Acacia species that are obligately inhabited by ants. Extrafloral nectar is secreted as an indirect resistance, attracting ants that defend plants against herbivores. Leaf damage induces extrafloral nectar secretion in several plant species; among these are various Acacia species and other Fabaceae investigated here. In contrast, Acacia species obligately inhabited by symbiotic ants nourish these ants by secreting extrafloral nectar constitutively at high rates that are not affected by leaf damage. The phylogeny of the genus Acacia and closely related genera indicate that the inducibility of extrafloral nectar is the plesiomorphic or 'original' state, whereas the constitutive extrafloral nectar flow is derived within Acacia. A constitutive resistance trait has evolved from an inducible one, obviously in response to particular functional demands.
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Affiliation(s)
- Martin Heil
- Department of Bioorganic Chemistry, Max-Planck-Institute for Chemical Ecology, Hans-Knöll-Strasse 8, Beutenberg Campus, D-07745 Jena, Germany.
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