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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
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Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
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Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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Kharabian-Masouleh A, Furtado A, Alsubaie B, Al-Dossary O, Wu A, Al-Mssalem I, Henry R. Loss of plastid ndh genes in an autotrophic desert plant. Comput Struct Biotechnol J 2023; 21:5016-5027. [PMID: 37867970 PMCID: PMC10589726 DOI: 10.1016/j.csbj.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023] Open
Abstract
Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.
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Affiliation(s)
- Ardashir Kharabian-Masouleh
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Bader Alsubaie
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Othman Al-Dossary
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Alex Wu
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Ibrahim Al-Mssalem
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Robert Henry
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
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Corvalán LCJ, Sobreiro MB, Carvalho LR, Dias RO, Braga-Ferreira RS, Targueta CP, Silva-Neto CME, Berton BW, Pereira AMS, Diniz-filho JAF, Telles MPC, Nunes R. Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1258794. [PMID: 37822334 PMCID: PMC10562606 DOI: 10.3389/fpls.2023.1258794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
Abstract
Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.
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Affiliation(s)
| | - Mariane B. Sobreiro
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Larissa R. Carvalho
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Renata O. Dias
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Ramilla S. Braga-Ferreira
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, Rondonópolis, Brazil
| | - Cintia P. Targueta
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | | | | | | | - José A. F. Diniz-filho
- Laboratório de Ecologia Teórica e Síntese, Universidade Federal de Goiás, Goiânia, Brazil
| | - Mariana P. C. Telles
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto Federal de Goiás, Goiás, Brazil
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Zoclanclounon YAB, Thamilarasan SK, Mo Y, Ahn BO, Kim JG, Lee K. Insights into chloroplast genome structure and phylogenetic relationships within the Sesamum species complex (Pedaliaceae). Front Genet 2023; 14:1207306. [PMID: 37323670 PMCID: PMC10267711 DOI: 10.3389/fgene.2023.1207306] [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: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Background: In the Sesamum species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships. Results: In the present study, we generated complete chloroplast genomes of six wild relatives (Sesamum alatum, Sesamum angolense, Sesamum pedaloides, Ceratotheca sesamoides (syn. Sesamum sesamoides), Ceratotheca triloba (syn. Sesamum trilobum), and Sesamum radiatum) and a Korean cultivar, Sesamum indicum cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863-153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including ndhA, ndhE, ndhF, ycf1, and psaC-ndhD. Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05 million years ago (Mya). In addition, S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others. Conclusion: Altogether, we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the Sesamum species complex.
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Affiliation(s)
- Yedomon Ange Bovys Zoclanclounon
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Senthil Kumar Thamilarasan
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Youngjun Mo
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byoung-Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Jeong-Gu Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Keunpyo Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
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Yu J, Li J, Zuo Y, Qin Q, Zeng S, Rennenberg H, Deng H. Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae). BMC PLANT BIOLOGY 2023; 23:132. [PMID: 36882685 PMCID: PMC9993602 DOI: 10.1186/s12870-023-04148-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/01/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. RESULTS In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. CONCLUSION These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.
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Affiliation(s)
- Jie Yu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
- No. 2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Jingling Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Youwei Zuo
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715 China
| | - Qiulin Qin
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Siyuan Zeng
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology, College of Resources and Environment, Southwest University, Chongqing, 400715 China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715 China
- No. 2 Tiansheng Road, Beibei District, Chongqing, 400716 China
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Sandoval-Padilla I, Zamora-Tavares MDP, Ruiz-Sánchez E, Pérez-Alquicira J, Vargas-Ponce O. Characterization of the plastome of Physaliscordata and comparative analysis of eight species of Physalis sensu stricto. PHYTOKEYS 2022; 210:109-134. [PMID: 36760406 PMCID: PMC9836641 DOI: 10.3897/phytokeys.210.85668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/07/2022] [Indexed: 06/18/2023]
Abstract
In this study, we sequenced, assembled, and annotated the plastome of Physaliscordata Mill. and compared it with seven species of the genus Physalis sensu stricto. Sequencing, annotating, and comparing plastomes allow us to understand the evolutionary mechanisms associated with physiological functions, select possible molecular markers, and identify the types of selection that have acted in different regions of the genome. The plastome of P.cordata is 157,000 bp long and presents the typical quadripartite structure with a large single-copy (LSC) region of 87,267 bp and a small single-copy (SSC) region of 18,501 bp, which are separated by two inverted repeat (IRs) regions of 25,616 bp each. These values are similar to those found in the other species, except for P.angulata L. and P.pruinosa L., which presented an expansion of the LSC region and a contraction of the IR regions. The plastome in all Physalis species studied shows variation in the boundary of the regions with three distinct types, the percentage of the sequence identity between coding and non-coding regions, and the number of repetitive regions and microsatellites. Four genes and 10 intergenic regions show promise as molecular markers and eight genes were under positive selection. The maximum likelihood analysis showed that the plastome is a good source of information for phylogenetic inference in the genus, given the high support values and absence of polytomies. In the Physalis plastomes analyzed here, the differences found, the positive selection of genes, and the phylogenetic relationships do not show trends that correspond to the biological or ecological characteristics of the species studied.
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Affiliation(s)
- Isaac Sandoval-Padilla
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - María del Pilar Zamora-Tavares
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Eduardo Ruiz-Sánchez
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Jessica Pérez-Alquicira
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
- Laboratorio Nacional de Identificación y Caracterización Vegetal A(LaniVeg), Consejo Nacional de Ciencia y Tecnología (CONACyT), Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoCONACYTMexico CityMexico
| | - Ofelia Vargas-Ponce
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
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Giorgashvili E, Reichel K, Caswara C, Kerimov V, Borsch T, Gruenstaeudl M. Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow Endemic Calligonum bakuense. FRONTIERS IN PLANT SCIENCE 2022; 13:779830. [PMID: 35874012 PMCID: PMC9296850 DOI: 10.3389/fpls.2022.779830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice.
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Affiliation(s)
- Eka Giorgashvili
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Katja Reichel
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Calvinna Caswara
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Vuqar Kerimov
- Institute of Botany, Azerbaijan National Academy of Sciences (ANAS), Baku, Azerbaijan
| | - Thomas Borsch
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Michael Gruenstaeudl
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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Hatami E, Jones KE, Kilian N. New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq). FRONTIERS IN PLANT SCIENCE 2022; 13:851716. [PMID: 35873957 PMCID: PMC9298463 DOI: 10.3389/fpls.2022.851716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1-3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.
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Affiliation(s)
- Elham Hatami
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Katy E. Jones
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Norbert Kilian
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
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A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae. Genes (Basel) 2022; 13:genes13040707. [PMID: 35456513 PMCID: PMC9032687 DOI: 10.3390/genes13040707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family.
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11
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Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects. Genes (Basel) 2022; 13:genes13030452. [PMID: 35328006 PMCID: PMC8952820 DOI: 10.3390/genes13030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.
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12
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Acha S, Majure LC. A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. Genes (Basel) 2022; 13:genes13020350. [PMID: 35205394 PMCID: PMC8871817 DOI: 10.3390/genes13020350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.
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13
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Dalla Costa TP, Silva MC, de Santana Lopes A, Gomes Pacheco T, de Oliveira JD, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes. PLANTA 2022; 255:57. [PMID: 35113261 DOI: 10.1007/s00425-022-03841-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.
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Affiliation(s)
- Tanara P Dalla Costa
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Maria C Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José D de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Valter A de Baura
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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14
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Chen J, Zhang S, Tang W, Du X, Yuan Y, Wu S. The complete chloroplast genome sequence of Opuntia sulphurea (Cactaceae). Mitochondrial DNA B Resour 2022; 7:361-362. [PMID: 35174291 PMCID: PMC8843126 DOI: 10.1080/23802359.2022.2035837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Opuntia sulphurea Gillies ex Salm-Dyck 1834 (Cactaceae) acts as an invasive species due to its ability to survive in various environments. In this study, we assembled the complete chloroplast (cp) genome of Opuntia sulphurea, which was 122,740 bp in length. The genome contained 100 genes, including 65 protein-coding genes, 31 tRNA genes and four rRNA genes. The base composition of the chloroplast genome was 32.11% A, 17.74% G, 18.34% C, and 31.80% T, resulting in an overall G + C content of 35.39%. A phylogenetic analysis across 23 species in Caryophyllales demonstrated a close relationship between Opuntia sulphurea and Opuntia quimilo.
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Affiliation(s)
- Jinyuan Chen
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
- College of Life Sciences, Qinghai Normal University, Xining, China
| | - Shangzhe Zhang
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Weidong Tang
- Gansu Desert Control Research Institute, Minqin Desert Botanical Garden, Wuwei, China
| | - Xin Du
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Yang Yuan
- Gansu Provincial Institute of Pharmaceutical Inspection, Lanzhou, China
| | - Shengdan Wu
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
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15
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Mutinda ES, Mkala EM, Dong X, Yang JX, Waswa EN, Nanjala C, Odago WO, Hu GW, Wang QF. Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia. PLANTS 2022; 11:231. [DOI: https:/doi.org/10.3390/plants11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.
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16
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Mutinda ES, Mkala EM, Dong X, Yang JX, Waswa EN, Nanjala C, Odago WO, Hu GW, Wang QF. Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia. PLANTS 2022; 11:plants11020231. [PMID: 35050119 PMCID: PMC8781850 DOI: 10.3390/plants11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.
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Affiliation(s)
- Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, Nairobi 451660-0100, Kenya
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Emmanuel Nyongesa Waswa
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wyclif Ochieng Odago
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, Nairobi 451660-0100, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.S.M.); (E.M.M.); (X.D.); (J.-X.Y.); (E.N.W.); (C.N.); (W.O.O.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Qin Q, Li J, Zeng S, Xu Y, Han F, Yu J. The complete plastomes of red fleshed pitaya ( Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:123-137. [PMID: 35221575 PMCID: PMC8847515 DOI: 10.1007/s12298-021-01121-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 06/01/2023]
Abstract
UNLABELLED Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we have reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandifloras, and S. validus) and carried out a comprehensive comparative analysis. All four Selenicereus plastomes have a typical quartile structure. The plastome size ranged from 133,146 to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the inverted repeat regions had undergone a dramatic expansion and formed a previously unreported small single copy/inverted repeat border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Our study enriches the plastome in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01121-z.
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Affiliation(s)
- Qiulin Qin
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | | | - Fang Han
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400716 China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716 China
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Könyves K, Bilsborrow J, Christodoulou MD, Culham A, David J. Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq. PeerJ 2021; 9:e12400. [PMID: 34824912 PMCID: PMC8592052 DOI: 10.7717/peerj.12400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.
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Affiliation(s)
- Kálmán Könyves
- Royal Horticultural Society Garden Wisley, Woking, United Kingdom
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Jordan Bilsborrow
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | | | - Alastair Culham
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - John David
- Royal Horticultural Society Garden Wisley, Woking, United Kingdom
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19
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Köhler M, Oakley LJ, Font F, Peñas MLL, Majure LC. On the continuum of evolution: a putative new hybrid speciation event in Opuntia (Cactaceae) between a native and an introduced species in southern South America. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1967510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| | - Luis J. Oakley
- Cátedra de Botánica, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
- Red List Authority Coordinator for the Temperate South American Plant Specialist Groups – International Union for Conservation of Nature (IUCN), Gland, Switzerland
| | - Fabián Font
- Herbario Museo de Farmacobotánica “Juan A. Domínguez” (BAF), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Laura Las Peñas
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Facultas de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba – CONICET, Córdoba, Argentina
| | - Lucas C. Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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20
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Mehl T, Gruenstaeudl M. airpg: automatically accessing the inverted repeats of archived plastid genomes. BMC Bioinformatics 2021; 22:413. [PMID: 34418956 PMCID: PMC8379869 DOI: 10.1186/s12859-021-04309-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 07/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations. RESULTS We introduce airpg, a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using airpg, followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations. CONCLUSION The number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. airpg enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index at http://pypi.python.org/pypi/airpg .
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Affiliation(s)
- Tilman Mehl
- Institut für Bioinformatik, Freie Universität Berlin, 14195 Berlin, Germany
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21
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Amaral DT, Bombonato JR, da Silva Andrade SC, Moraes EM, Franco FF. The genome of a thorny species: comparative genomic analysis among South and North American Cactaceae. PLANTA 2021; 254:44. [PMID: 34357508 DOI: 10.1007/s00425-021-03690-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
The first South American cactus nuclear genome assembly associated with comparative genomic analyses provides insights into nuclear and plastid genomic features, such as size, transposable elements, and metabolic processes related to cactus development. Here, we assembled the partial genome, plastome, and transcriptome of Cereus fernambucensis (Cereeae, Cactaceae), a representative species of the South American core Cactoideae. We accessed other genomes and transcriptomes available for cactus species to compare the heterozygosity level, genome size, transposable elements, orthologous genes, and plastome structure. These estimates were obtained from the literature or using the same pipeline adopted for C. fermabucensis. In addition to the C. fernambucensis plastome, we also performed de novo plastome assembly of Pachycereus pringlei, Stenocereus thurberi, and Pereskia humboldtii based on the sequences available in public databases. We estimated a genome size of ~ 1.58 Gb for C. fernambucensis, the largest genome among the compared species. The genome heterozygosity was 0.88% in C. fernambucensis but ranged from 0.36 (Carnegiea gigantea) to 17.4% (Lophocereus schottii) in the other taxa. The genome lengths of the studied cacti are constituted by a high amount of transposable elements, ranging from ~ 57 to ~ 67%. Putative satellite DNAs are present in all species, excepting C. gigantea. The plastome of C. fernambucensis was ~ 104 kb, showing events of translocation, inversion, and gene loss. We observed a low number of shared unique orthologs, which may suggest gene duplication events and the simultaneous expression of paralogous genes. We recovered 37 genes that have undergone positive selection along the Cereus branch that are associated with different metabolic processes, such as improving photosynthesis during drought stress and nutrient absorption, which may be related to the adaptation to xeric areas of the Neotropics.
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Affiliation(s)
- Danilo Trabuco Amaral
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
- Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Juliana Rodrigues Bombonato
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
- Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Sónia Cristina da Silva Andrade
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Evandro Marsola Moraes
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil
| | - Fernando Faria Franco
- Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil.
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22
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Zheng J, Meinhardt LW, Goenaga R, Zhang D, Yin Y. The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes. HORTICULTURE RESEARCH 2021; 8:63. [PMID: 33750805 PMCID: PMC7943767 DOI: 10.1038/s41438-021-00501-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 05/05/2023]
Abstract
Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.
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Affiliation(s)
- Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE, 68588, USA
| | | | - Ricardo Goenaga
- Tropical Agriculture Research Station, USDA-ARS, Puerto Rico, PR, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Lab, USDA-ARS, Beltsville, MD, USA.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE, 68588, USA.
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23
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Majure LC, Barrios D, Díaz E, Zumwalde BA, Testo W, Negrón-Ortíz V. Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular, giant Consolea (Opuntioideae). AMERICAN JOURNAL OF BOTANY 2021; 108:200-215. [PMID: 33598914 DOI: 10.1002/ajb2.1610] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
PREMISE The Caribbean islands are in the top five biodiversity hotspots on the planet; however, the biogeographic history of the seasonally dry tropical forest (SDTF) there is poorly studied. Consolea consists of nine species of dioecious, hummingbird-pollinated tree cacti endemic to the West Indies, which form a conspicuous element of the SDTF. Several species are threatened by anthropogenic disturbance, disease, sea-level rise, and invasive species and are of conservation concern. However, no comprehensive phylogeny yet exists for the clade. METHODS We reconstructed the phylogeny of Consolea, sampling all species using plastomic data to determine relationships, understand the evolution of key morphological characters, and test their biogeographic history. We estimated divergence times to determine the role climate change may have played in shaping the current diversity of the clade. RESULTS Consolea appears to have evolved very recently during the latter part of the Pleistocene on Cuba/Hispaniola likely from a South American ancestor and, from there, moved into the Bahamas, Jamaica, Puerto Rico, Florida, and the Lesser Antilles. The tree growth form is a synapomorphy of Consolea and likely aided in the establishment and diversification of the clade. CONCLUSIONS Pleistocene aridification associated with glaciation likely played a role in shaping the current diversity of Consolea, and insular gigantism may have been a key innovation leading to the success of these species to invade the often-dense SDTF. This in-situ Caribbean radiation provides a window into the generation of species diversity and the complexity of the SDTF community within the Antilles.
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Affiliation(s)
- Lucas C Majure
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, 85008, USA
| | - Duniel Barrios
- Grupo de Ecología y Conservación, Jardín Botánico Nacional, Universidad de La Habana, Cuba
| | - Edgardo Díaz
- Planta! - Plantlife Conservation Society, Vancouver, BC, Canada
| | - Bethany A Zumwalde
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Weston Testo
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Vivian Negrón-Ortíz
- U.S. Fish and Wildlife Service, 1601 Balboa Ave., Panama City, FL, 32405, USA
- Department of Biology, Miami University, Oxford, OH, 45056, USA
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24
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Majure LC, Encarnación Y, Clase T, Peguero B, Ho K, Barrios D. Phylogenetics of Leptocereus (Cactaceae) on Hispaniola: clarifying species limits in the L. weingartianus complex and a new species from the Sierra de Bahoruco. PHYTOKEYS 2021; 172:17-37. [PMID: 33597828 PMCID: PMC7864899 DOI: 10.3897/phytokeys.172.59497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/15/2020] [Indexed: 05/08/2023]
Abstract
The Antillean genus Leptocereus represents an in-situ radiation among the Greater and Lesser Antilles of 19 currently recognized species. Extensive fieldwork carried out in the Dominican Republic over recent years has revealed that the species limits of Leptocereus of Hispaniola are more complex than previously thought. There are four currently recognized species that occur on the island, L. demissus, L. paniculatus, L. undulosus and L. weingartianus. We evaluate species limits in this group based on DNA sequence data and phylogenetic analysis, morphological characters and a survey of herbarium specimens from across Hispaniola. Based on our analyses, it is clear that at least five species occur on the island of Hispaniola, with the new species from Sierra de Bahoruco, L. velozianus, described here. We provide an identification key, distribution maps and photographic plates for all species on Hispaniola based on our own fieldwork and the study of herbarium specimens. The description of yet another species of Leptocereus on Hispaniola reiterates the importance of the poorly studied, but yet biodiverse, seasonally dry tropical forest in the Antilles.
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Affiliation(s)
- Lucas C. Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL 32611, USA
| | - Yuley Encarnación
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Teodoro Clase
- Departamento de Botánica, Jardín Botánico Nacional “Dr. Rafael M. Moscoso”, Santo Domingo, Dominican Republic
| | - Brígido Peguero
- Departamento de Botánica, Jardín Botánico Nacional “Dr. Rafael M. Moscoso”, Santo Domingo, Dominican Republic
| | - Kelly Ho
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Duniel Barrios
- Grupo de Ecología y Conservación, Jardín Botánico Nacional, Universidad de La Habana, Habana, Cuba
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25
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Wei N, Pérez-Escobar OA, Musili PM, Huang WC, Yang JB, Hu AQ, Hu GW, Grace OM, Wang QF. Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region. FRONTIERS IN PLANT SCIENCE 2021; 12:712064. [PMID: 34421963 PMCID: PMC8372406 DOI: 10.3389/fpls.2021.712064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 05/09/2023]
Abstract
With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.
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Affiliation(s)
- Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Paul M. Musili
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Wei-Chang Huang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Olwen M. Grace
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- *Correspondence: Olwen M. Grace,
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Qing-Feng Wang,
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26
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Rono PC, Dong X, Yang JX, Mutie FM, Oulo MA, Malombe I, Kirika PM, Hu GW, Wang QF. Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships. Front Genet 2020; 11:560368. [PMID: 33362846 PMCID: PMC7756076 DOI: 10.3389/fgene.2020.560368] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.
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Affiliation(s)
- Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Millicent A Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Paul M Kirika
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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27
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Oulo MA, Yang JX, Dong X, Wanga VO, Mkala EM, Munyao JN, Onjolo VO, Rono PC, Hu GW, Wang QF. Complete Chloroplast Genome of Rhipsalis baccifera, the only Cactus with Natural Distribution in the Old World: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies. PLANTS (BASEL, SWITZERLAND) 2020; 9:E979. [PMID: 32752116 PMCID: PMC7464518 DOI: 10.3390/plants9080979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 01/29/2023]
Abstract
Rhipsalis baccifera is the only cactus that naturally occurs in both the New World and the Old World, and has thus drawn the attention of most researchers. The complete chloroplast (cp) genome of R. baccifera is reported here for the first time. The cp genome of R. baccifera has 122, 333 base pairs (bp), with a large single-copy (LSC) region (81,459 bp), SSC (23,531 bp) and two inverted repeat (IR) regions each 8530 bp. The genome contains 110 genes, with 73 protein-coding genes, 31 tRNAs, 4 rRNAs and 2 pseudogenes. Twelve genes have introns, with loss of introns being observed in, rpoc1clpP and rps12 genes. 49 repeat sequences and 62 simple sequence repeats (SSRs) were found in the genome. Comparative analysis with eight species of the ACPT (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae) clade of the suborder Portulacineae species, showed that R. baccifera genome has higher number of rearrangements, with a 19 gene inversion in its LSC region representing the most significant structural change in terms of its size. Inversion of the SSC region seems common in subfamily Cactoideae, and another 6 kb gene inversion between rbcL- trnM was observed in R. baccifera and Carnegiea gigantea. The IRs of R. baccifera are contracted. The phylogenetic analysis among 36 complete chloroplast genomes of Caryophyllales species and two outgroup species supported monophyly of the families of the ACPT clade. R. baccifera occupied a basal position of the family Cactaceae clade in the tree. A high number of rearrangements in this cp genome suggests a larger number mutation events in the history of evolution of R. baccifera. These results provide important tools for future work on R. baccifera and in the evolutionary studies of the suborder Portulacineae.
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Affiliation(s)
- Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jacinta Ndunge Munyao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Victor Omondi Onjolo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (M.A.O.); (J.-X.Y.); (X.D.); (V.O.W.); (E.M.M.); (J.N.M.); (V.O.O.); (P.C.R.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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