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Nyree J. C. Zerega - One of the best experts on this subject based on the ideXlab platform.
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paralogs and off target sequences improve phylogenetic resolution in a densely sampled study of the breadfruit genus Artocarpus moraceae
Systematic Biology, 2021Co-Authors: Elliot M. Gardner, Matthew G Johnson, Joan T Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Norman J Wickett, Nyree J. C. ZeregaAbstract:We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets increased convergence between analysis methods but did not reduce gene-tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. Although the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of data sets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.]
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two new species of Artocarpus moraceae from thailand and vietnam
Phytotaxa, 2020Co-Authors: Elliot M. Gardner, Arunrat Chaveerach, Runglawan Sudmoon, Nyree J. C. ZeregaAbstract:Recent taxonomic work on Artoarpus has revealed two undescribed species from Thailand and Vietnam. Artocarpus rubrosoccatus , endemic to peninsular Thailand, resembles A. lacucha but is distinguished by its deep red clavate staminate inflorescences. Artocarpus montanus is found in the montane regions of southern and central Vietnam, and perhaps also in Thailand. This species resembles the vegetative parts of A. lowii and A. excelsus , but A. montanus differs in its longer syncarp processes and its geographic distribution. The vast majority of Artocarpus species are found in tropical lowlands, and A. montanus , along with A. excelsus, represent the only known members of the genus that are restricted to montane habitats. The provisional conservation assessment of both new species is Near Threatened, because although their known areas of occupancy are restricted, both occur in protected areas.
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paralogs and off target sequences improve phylogenetic resolution in a densely sampled study of the breadfruit genus Artocarpus moraceae
Unknown Journal, 2019Co-Authors: Elliot M. Gardner, Matthew G Johnson, Joan T Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Norman J Wickett, Nyree J. C. ZeregaAbstract:We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.
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a flower in fruit s clothing pollination of jackfruit Artocarpus heterophyllus moraceae by a new species of gall midge clinodiplosis ultracrepidata sp nov diptera cecidomyiidae
International Journal of Plant Sciences, 2018Co-Authors: Elliot M. Gardner, Raymond J. Gagné, Paul E. Kendra, Wayne S. Montgomery, Robert A. Raguso, Tashina T. Mcneil, Nyree J. C. ZeregaAbstract:Premise of research. Jackfruit (Artocarpus heterophyllus, Moraceae) is an emerging but underutilized crop whose pollination is poorly understood. We present a multidisciplinary investigation of the...
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hybpiper extracting coding sequence and introns for phylogenetics from high throughput sequencing reads using target enrichment
Applications in Plant Sciences, 2016Co-Authors: Matthew G Johnson, Elliot M. Gardner, Nyree J. C. Zerega, Yang Liu, Rafael Medina, Bernard Goffinet, Jonathan A Shaw, Norman J WickettAbstract:Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely ...
Elliot M. Gardner - One of the best experts on this subject based on the ideXlab platform.
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paralogs and off target sequences improve phylogenetic resolution in a densely sampled study of the breadfruit genus Artocarpus moraceae
Systematic Biology, 2021Co-Authors: Elliot M. Gardner, Matthew G Johnson, Joan T Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Norman J Wickett, Nyree J. C. ZeregaAbstract:We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets increased convergence between analysis methods but did not reduce gene-tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. Although the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of data sets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.]
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two new species of Artocarpus moraceae from thailand and vietnam
Phytotaxa, 2020Co-Authors: Elliot M. Gardner, Arunrat Chaveerach, Runglawan Sudmoon, Nyree J. C. ZeregaAbstract:Recent taxonomic work on Artoarpus has revealed two undescribed species from Thailand and Vietnam. Artocarpus rubrosoccatus , endemic to peninsular Thailand, resembles A. lacucha but is distinguished by its deep red clavate staminate inflorescences. Artocarpus montanus is found in the montane regions of southern and central Vietnam, and perhaps also in Thailand. This species resembles the vegetative parts of A. lowii and A. excelsus , but A. montanus differs in its longer syncarp processes and its geographic distribution. The vast majority of Artocarpus species are found in tropical lowlands, and A. montanus , along with A. excelsus, represent the only known members of the genus that are restricted to montane habitats. The provisional conservation assessment of both new species is Near Threatened, because although their known areas of occupancy are restricted, both occur in protected areas.
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paralogs and off target sequences improve phylogenetic resolution in a densely sampled study of the breadfruit genus Artocarpus moraceae
Unknown Journal, 2019Co-Authors: Elliot M. Gardner, Matthew G Johnson, Joan T Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Norman J Wickett, Nyree J. C. ZeregaAbstract:We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.
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a flower in fruit s clothing pollination of jackfruit Artocarpus heterophyllus moraceae by a new species of gall midge clinodiplosis ultracrepidata sp nov diptera cecidomyiidae
International Journal of Plant Sciences, 2018Co-Authors: Elliot M. Gardner, Raymond J. Gagné, Paul E. Kendra, Wayne S. Montgomery, Robert A. Raguso, Tashina T. Mcneil, Nyree J. C. ZeregaAbstract:Premise of research. Jackfruit (Artocarpus heterophyllus, Moraceae) is an emerging but underutilized crop whose pollination is poorly understood. We present a multidisciplinary investigation of the...
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hybpiper extracting coding sequence and introns for phylogenetics from high throughput sequencing reads using target enrichment
Applications in Plant Sciences, 2016Co-Authors: Matthew G Johnson, Elliot M. Gardner, Nyree J. C. Zerega, Yang Liu, Rafael Medina, Bernard Goffinet, Jonathan A Shaw, Norman J WickettAbstract:Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely ...
Diane Ragone - One of the best experts on this subject based on the ideXlab platform.
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Chloroplast Microsatellite Markers for Artocarpus (Moraceae) Developed from Transcriptome Sequences
Applications in plant sciences, 2015Co-Authors: Elliot M. Gardner, Diane Ragone, Kristen M. Laricchia, Matthew D. Murphy, Brian E. Scheffler, Sheron A. Simpson, Evelyn W. Williams, Nyree J. C. ZeregaAbstract:Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. Conclusions: These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in...
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Diversity in the breadfruit complex (Artocarpus, Moraceae): genetic characterization of critical germplasm
Tree Genetics & Genomes, 2015Co-Authors: Nyree Zerega, Diane Ragone, Tyr Wiesner-hanks, Brian Irish, Brian Scheffler, Sheron Simpson, Francis ZeeAbstract:Breadfruit ( Artocarpus altilis , Moraceae) is a traditional staple crop in Oceania and has been introduced throughout the tropics. This study examines important germplasm collections of breadfruit and its closest wild relatives and aims to (1) characterize genetic diversity, including identification of unknown and duplicate accessions, (2) evaluate genetic structure and hybridization within the breadfruit complex, and (3) compare utility of microsatellite markers to previously reported amplified fragment length polymorphism (AFLP) and isozyme markers in differentiating among cultivars. Data for 19 microsatellite loci were collected for 349 individuals (representing 255 accessions) including breadfruit ( A. altilis ), two wild relatives ( Artocarpus camansi and Artocarpus mariannensis ), and putative hybrids ( A. altilis × A. mariannensis ). Accessions were of mixed ploidy and regional origin, but predominantly from Oceania. Microsatellite loci collectively had a polymorphic information content (PIC) of 0.627 and distinguished 197 unique genotypes sorted into 129 different lineages, but a single genotype accounts for 49 % of all triploid breadfruit examined. Triploid hybrids and diploid A. altilis exhibited the highest levels of diversity as measured by allele number and gene diversity. Most accessions (75 %) of unknown origin matched either a known genotype or lineage group in the collection. Putative hybrids all had genetic contributions from A. mariannensis but ranged in the level of genetic contribution from A. altilis . Microsatellite markers were found to be more informative than isozyme markers and slightly less informative, with regard to accession discrimination, than AFLP markers. This set of microsatellite markers and the dataset presented here will be valuable for breadfruit germplasm management and conservation.
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Artocarpus camansi breadnut
2006Co-Authors: Diane RagoneAbstract:IN BRIEF Distribution Currently found throughout the tropics, including some Pacific islands. Size Medium tree 15 m (50 ft) or more in height at maturity. Habitat Grows best in equatorial lowlands below 600–650 m (1970–2130 ft) and rainfall of 1300–3800 mm (50–150 in) but is widely adaptable. Vegetation In native range, an important component of the vegetation associated with lowland mixed alluvial forests; in cultivation, associated with a wide variety of domesticated plants. Soils Deep, fertile, well drained soils are pre ferred. Growth rate Moderately fast growing in fa vorable conditions, growing 0.5–1.5 m (1.5–5 ft) per year. Main agroforestry uses Overstory, home gardens. Main products Staple food, wood for crafts. Yields Mature trees can yield 600–800 fruits per season. Intercropping Interplanted with small fruit trees or shortterm fruit and vegetable crops. Invasive potential It has little potential for invasiveness. Species Profiles for Pacific Island Agroforestry www.traditionaltree.org April 2006 ver. 2.1
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chromosome numbers and pollen stainability of three species of pacific island breadfruit Artocarpus moraceae
American Journal of Botany, 2001Co-Authors: Diane RagoneAbstract:Chromosome numbers were determined for 48 accessions of breadfruit (Artocarpus altilis, A. mariannensis, and A. camnansi [Moraceae]) from 16 Pacific Island groups, Indonesia, and the Philippines. Artocarpus camansi and A. mariannensis exhibit counts of 2n = 56; 2n = 56 (diploidy) and 2n = 84 (triploidy) were observed for A. altilis. Most diploid cultivars of A. altilis were seeded, but two cultivars with reduced seed number were observed. Micronesian accessions included putative interspecific hybrids between A. altilis and A. mariannensis. The majority of these accessions were seedless diploids, but triploid putative hybrids were also observed. Pollen stainablility was shown to correlate with the degree of seediness. Breadfruit is an important staple food crop in the Pacific islands where two species, including numerous cultivars, are recognized and grown (Parham, 1966; Ragone, 1995, 1997). Artocarpus altilis (Park.) Fosberg [synonyms A. communis J. R. & G. Forster, A. incisus (Thunb.) L. f.] is the most widely distributed and exhibits great variability. This species includes both seedless and seeded forms with seeded types most common in the western South Pacific. Seedless cultivars are most common in Micronesia and the eastern islands of Polynesia. Artocarpus mariannensis Trecul is always seeded and grows wild on the uplifted rock islands of Palau and the limestone ridges of the Mariana Islands. A few cultivated trees can be found growing throughout the islands of Micronesia, especially on coral atolls. It is not found in Melanesia or Polynesia other than the islands of Tokelau and Tuvalu. Fosberg (1960) suggested that introgression between A. altilis and A. mariannensis may have occurred in Micronesia, and there are many
O T Ogunmodede - One of the best experts on this subject based on the ideXlab platform.
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ameliorative activity of ethanolic extract of Artocarpus heterophyllus stem bark on alloxan induced diabetic rats
Advanced Pharmaceutical Bulletin, 2018Co-Authors: Basiru Olaitan Ajiboye, Oluwafemi Adeleke Ojo, Oluwatosin Adeyonu, Oluwatosin Debbie Imiere, Babatunji Emmanuel Oyinloye, O T OgunmodedeAbstract:Purpose: Diabetes mellitus is one of the major endocrine disorders, characterized by impaired insulin action and deficiency. Traditionally, Artocarpus heterophyllus stem bark has been reputably used in the management of diabetes mellitus and its complications. The present study evaluates the ameliorative activity of ethanol extract of Artocarpus heterophyllus stem bark in alloxan-induced diabetic rats. Methods: Diabetes mellitus was induced by single intraperitoneal injection of 150 mg/kg body weight of alloxan and the animals were orally administered with 50, 100 and 150 mg/kg body weight ethanol extract of Artocarpus heterophyllus stem bark once daily for 21 days. Results: At the end of the intervention, diabetic control rats showed significant (p 0.05) different with non-diabetic rats. Conclusion: The results suggest that ethanol extract of Artocarpus heterophyllus stem bark may be useful in ameliorating complications associated with diabetes mellitus patients.
Oluwafemi Adeleke Ojo - One of the best experts on this subject based on the ideXlab platform.
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ameliorative activity of ethanolic extract of Artocarpus heterophyllus stem bark on alloxan induced diabetic rats
Advanced Pharmaceutical Bulletin, 2018Co-Authors: Basiru Olaitan Ajiboye, Oluwafemi Adeleke Ojo, Oluwatosin Adeyonu, Oluwatosin Debbie Imiere, Babatunji Emmanuel Oyinloye, O T OgunmodedeAbstract:Purpose: Diabetes mellitus is one of the major endocrine disorders, characterized by impaired insulin action and deficiency. Traditionally, Artocarpus heterophyllus stem bark has been reputably used in the management of diabetes mellitus and its complications. The present study evaluates the ameliorative activity of ethanol extract of Artocarpus heterophyllus stem bark in alloxan-induced diabetic rats. Methods: Diabetes mellitus was induced by single intraperitoneal injection of 150 mg/kg body weight of alloxan and the animals were orally administered with 50, 100 and 150 mg/kg body weight ethanol extract of Artocarpus heterophyllus stem bark once daily for 21 days. Results: At the end of the intervention, diabetic control rats showed significant (p 0.05) different with non-diabetic rats. Conclusion: The results suggest that ethanol extract of Artocarpus heterophyllus stem bark may be useful in ameliorating complications associated with diabetes mellitus patients.
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effect of Artocarpus altilis fruit based diet on liver and kidney function indices on alloxan induced diabetic rats
Mediterranean Journal of Nutrition and Metabolism, 2016Co-Authors: Bashir Ajiboye, Oluwafemi Adeleke Ojo, G S Chikezie, I Y Aganzi, S A Onikanni, Olakunle Bamikole Afolabi, Scholastica O Anadozie, O SobajoAbstract:BACKGROUND: The prevalence of diabetes mellitus continues to increase alarmingly in spite of years of intensive research. The need to explore alternative therapy such dietary and phytotherapy has been gaining attention in the management/treatment of diabetes mellitus. OBJECTIVE: The present research work was carried out to investigate the biochemical indices in the liver and kidney of alloxan-induced diabetic rats fed with Artocarpus altilis fruit based-diet. METHODS: Diabetes was induced by a single intraperitoneal injection of alloxan (150 mg/kg) in albino rats. A total of thirty two albino rats (Rattus norvegicus) were grouped into four; control (non-diabetic rat), diabetic untreated rats, diabetic rats administered with metformin daily and diabetic rats fed with Artocarpus altilis fruit based-diet groups. Biochemical indices in the serum, liver and kidney were determined. RESULTS: The results shows significant (P < 0.05) decrease in alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, bilirubin, urea, creatinine and lipid peroxidation of diabetic fed with Artocarpus altilis fruit based-diet. Also diabetic rats fed with Artocarpus altilis fruit based-diet demonstrated significant increase (p < 0.05) in albumin and total protein concentrations as well as antioxidant enzymes activities when compared with diabetic untreated rats and diabetic rats administered with metformin daily. CONCLUSION: The results obtained in this study demonstrated that consumption of Artocarpus altilis fruit based-diet may ameliorate the liver and kidney function indices of alloxan-induced diabetic rats.
