The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Guixi Wang - One of the best experts on this subject based on the ideXlab platform.
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multilocus data reveal deep phylogenetic relationships and intercontinental biogeography of the eurasian north american genus Corylus betulaceae
Molecular Phylogenetics and Evolution, 2020Co-Authors: Tiantian Zhao, Lisong Liang, Guixi Wang, Zhen YangAbstract:Abstract The evolutionary history of the genus Corylus, a tertiary disjunct lineage consisting of approximately 15–20 taxa with New and Old World distribution, has not been fully studied using molecular tools. In this research, we reconstructed comprehensive phylogenies of this genus using multiple datasets (genome-wide SNPs; complete chloroplast genomes; and nuclear ribosomal ITS sequences) based on detailed sampling of 17 Corylus species currently recognized. Divergence times were estimated using a fossil calibrated relaxed clock model, and ancestral area reconstruction were inferred using Bayesian binary MCMC (BBM) method and the dispersal–extinction–cladogenesis (DEC) model. Phylogenetic incongruences were detected from datasets, with nuclear SNP and ITS phylogenies supporting four major clades that correspond well with morphological traits, while chloroplast phylogeny revealed geographic partitioning. Recombination and introgressive hybridization played important roles in Corylus diversification. Molecular dating and biogeographical analyses unambiguously revealed that Corylus originated in Southwest China during the middle Eocene. The westward migration of Phyllochlamys (Clade C) and Colurnae (Clade D) and the uplift of Qinghai-Tibet Plateau drove the formation of European taxa, whereas the transoccanic migration crossing the Bering Land Bridge of Siphonochlamys (Clade B) and Phyllochlamys (Clade C) led to the occurrence of North American taxa. The topographic heterogeneity and climatic oscillations from Miocene to Pleistocene made East Asia the diversity center for Corylus. This study offers important insights into the phylogenetic relationships and biogeography history of the genus Corylus.
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resolving the speciation patterns and evolutionary history of the intercontinental disjunct genus Corylus betulaceae using genome wide snps
Frontiers in Plant Science, 2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Understanding the underlying mechanisms of species origin, divergence, and distribution patterns of the intercontinental disjunct taxa has long fascinated botanists. Based on 4,894 genome-wide single-nucleotide polymorphism dataset, we present a molecular phylogenetic reconstruction of genus Corylus (Betulaceae), which have a disjunct distribution between Eurasia and North America (NA). The aim is to explore the speciation patterns and evolutionary relationships of Corylus species by establishing a general phylogenetic framework with extensive sampling. Both the molecular phylogeny inferred from recombination-free dataset and structure analysis support the division of Corylus into four major clades (A-D). Recombination tests and hybridization detection reveal extensive recombination and hybridization events among different clades, which have potentially influenced the speciation process of Corylus. Divergence time estimation indicates that recent common ancestor (MRCA) of Corylus occurred in late Eocene (∼36.38 Ma) and subsequent rapid diversification began during Miocene. Ancestral area reconstruction shows that Corylus originated from southwest China. The arrival of two clades (Clades B and C) to NA was well supported by the long distance dispersal crossing the Bering land bridge. The Himalayas, European-Mediterranean area, and other distribution regions are primarily the recipients of dispersal taxa. Vicariance after dispersal plays an important role in speciation.
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comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus betulaceae species
Frontiers in Plant Science, 2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.
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Table_1_Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species.XLSX
2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.
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Table_1_Resolving the Speciation Patterns and Evolutionary History of the Intercontinental Disjunct Genus Corylus (Betulaceae) Using Genome-Wide SNPs.XLSX
2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Understanding the underlying mechanisms of species origin, divergence, and distribution patterns of the intercontinental disjunct taxa has long fascinated botanists. Based on 4,894 genome-wide single-nucleotide polymorphism dataset, we present a molecular phylogenetic reconstruction of genus Corylus (Betulaceae), which have a disjunct distribution between Eurasia and North America (NA). The aim is to explore the speciation patterns and evolutionary relationships of Corylus species by establishing a general phylogenetic framework with extensive sampling. Both the molecular phylogeny inferred from recombination-free dataset and structure analysis support the division of Corylus into four major clades (A–D). Recombination tests and hybridization detection reveal extensive recombination and hybridization events among different clades, which have potentially influenced the speciation process of Corylus. Divergence time estimation indicates that recent common ancestor (MRCA) of Corylus occurred in late Eocene (∼36.38 Ma) and subsequent rapid diversification began during Miocene. Ancestral area reconstruction shows that Corylus originated from southwest China. The arrival of two clades (Clades B and C) to NA was well supported by the long distance dispersal crossing the Bering land bridge. The Himalayas, European-Mediterranean area, and other distribution regions are primarily the recipients of dispersal taxa. Vicariance after dispersal plays an important role in speciation.
Zhen Yang - One of the best experts on this subject based on the ideXlab platform.
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multilocus data reveal deep phylogenetic relationships and intercontinental biogeography of the eurasian north american genus Corylus betulaceae
Molecular Phylogenetics and Evolution, 2020Co-Authors: Tiantian Zhao, Lisong Liang, Guixi Wang, Zhen YangAbstract:Abstract The evolutionary history of the genus Corylus, a tertiary disjunct lineage consisting of approximately 15–20 taxa with New and Old World distribution, has not been fully studied using molecular tools. In this research, we reconstructed comprehensive phylogenies of this genus using multiple datasets (genome-wide SNPs; complete chloroplast genomes; and nuclear ribosomal ITS sequences) based on detailed sampling of 17 Corylus species currently recognized. Divergence times were estimated using a fossil calibrated relaxed clock model, and ancestral area reconstruction were inferred using Bayesian binary MCMC (BBM) method and the dispersal–extinction–cladogenesis (DEC) model. Phylogenetic incongruences were detected from datasets, with nuclear SNP and ITS phylogenies supporting four major clades that correspond well with morphological traits, while chloroplast phylogeny revealed geographic partitioning. Recombination and introgressive hybridization played important roles in Corylus diversification. Molecular dating and biogeographical analyses unambiguously revealed that Corylus originated in Southwest China during the middle Eocene. The westward migration of Phyllochlamys (Clade C) and Colurnae (Clade D) and the uplift of Qinghai-Tibet Plateau drove the formation of European taxa, whereas the transoccanic migration crossing the Bering Land Bridge of Siphonochlamys (Clade B) and Phyllochlamys (Clade C) led to the occurrence of North American taxa. The topographic heterogeneity and climatic oscillations from Miocene to Pleistocene made East Asia the diversity center for Corylus. This study offers important insights into the phylogenetic relationships and biogeography history of the genus Corylus.
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resolving the speciation patterns and evolutionary history of the intercontinental disjunct genus Corylus betulaceae using genome wide snps
Frontiers in Plant Science, 2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Understanding the underlying mechanisms of species origin, divergence, and distribution patterns of the intercontinental disjunct taxa has long fascinated botanists. Based on 4,894 genome-wide single-nucleotide polymorphism dataset, we present a molecular phylogenetic reconstruction of genus Corylus (Betulaceae), which have a disjunct distribution between Eurasia and North America (NA). The aim is to explore the speciation patterns and evolutionary relationships of Corylus species by establishing a general phylogenetic framework with extensive sampling. Both the molecular phylogeny inferred from recombination-free dataset and structure analysis support the division of Corylus into four major clades (A-D). Recombination tests and hybridization detection reveal extensive recombination and hybridization events among different clades, which have potentially influenced the speciation process of Corylus. Divergence time estimation indicates that recent common ancestor (MRCA) of Corylus occurred in late Eocene (∼36.38 Ma) and subsequent rapid diversification began during Miocene. Ancestral area reconstruction shows that Corylus originated from southwest China. The arrival of two clades (Clades B and C) to NA was well supported by the long distance dispersal crossing the Bering land bridge. The Himalayas, European-Mediterranean area, and other distribution regions are primarily the recipients of dispersal taxa. Vicariance after dispersal plays an important role in speciation.
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comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus betulaceae species
Frontiers in Plant Science, 2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.
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Table_1_Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species.XLSX
2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.
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Table_1_Resolving the Speciation Patterns and Evolutionary History of the Intercontinental Disjunct Genus Corylus (Betulaceae) Using Genome-Wide SNPs.XLSX
2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Understanding the underlying mechanisms of species origin, divergence, and distribution patterns of the intercontinental disjunct taxa has long fascinated botanists. Based on 4,894 genome-wide single-nucleotide polymorphism dataset, we present a molecular phylogenetic reconstruction of genus Corylus (Betulaceae), which have a disjunct distribution between Eurasia and North America (NA). The aim is to explore the speciation patterns and evolutionary relationships of Corylus species by establishing a general phylogenetic framework with extensive sampling. Both the molecular phylogeny inferred from recombination-free dataset and structure analysis support the division of Corylus into four major clades (A–D). Recombination tests and hybridization detection reveal extensive recombination and hybridization events among different clades, which have potentially influenced the speciation process of Corylus. Divergence time estimation indicates that recent common ancestor (MRCA) of Corylus occurred in late Eocene (∼36.38 Ma) and subsequent rapid diversification began during Miocene. Ancestral area reconstruction shows that Corylus originated from southwest China. The arrival of two clades (Clades B and C) to NA was well supported by the long distance dispersal crossing the Bering land bridge. The Himalayas, European-Mediterranean area, and other distribution regions are primarily the recipients of dispersal taxa. Vicariance after dispersal plays an important role in speciation.
Tiantian Zhao - One of the best experts on this subject based on the ideXlab platform.
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multilocus data reveal deep phylogenetic relationships and intercontinental biogeography of the eurasian north american genus Corylus betulaceae
Molecular Phylogenetics and Evolution, 2020Co-Authors: Tiantian Zhao, Lisong Liang, Guixi Wang, Zhen YangAbstract:Abstract The evolutionary history of the genus Corylus, a tertiary disjunct lineage consisting of approximately 15–20 taxa with New and Old World distribution, has not been fully studied using molecular tools. In this research, we reconstructed comprehensive phylogenies of this genus using multiple datasets (genome-wide SNPs; complete chloroplast genomes; and nuclear ribosomal ITS sequences) based on detailed sampling of 17 Corylus species currently recognized. Divergence times were estimated using a fossil calibrated relaxed clock model, and ancestral area reconstruction were inferred using Bayesian binary MCMC (BBM) method and the dispersal–extinction–cladogenesis (DEC) model. Phylogenetic incongruences were detected from datasets, with nuclear SNP and ITS phylogenies supporting four major clades that correspond well with morphological traits, while chloroplast phylogeny revealed geographic partitioning. Recombination and introgressive hybridization played important roles in Corylus diversification. Molecular dating and biogeographical analyses unambiguously revealed that Corylus originated in Southwest China during the middle Eocene. The westward migration of Phyllochlamys (Clade C) and Colurnae (Clade D) and the uplift of Qinghai-Tibet Plateau drove the formation of European taxa, whereas the transoccanic migration crossing the Bering Land Bridge of Siphonochlamys (Clade B) and Phyllochlamys (Clade C) led to the occurrence of North American taxa. The topographic heterogeneity and climatic oscillations from Miocene to Pleistocene made East Asia the diversity center for Corylus. This study offers important insights into the phylogenetic relationships and biogeography history of the genus Corylus.
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resolving the speciation patterns and evolutionary history of the intercontinental disjunct genus Corylus betulaceae using genome wide snps
Frontiers in Plant Science, 2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Understanding the underlying mechanisms of species origin, divergence, and distribution patterns of the intercontinental disjunct taxa has long fascinated botanists. Based on 4,894 genome-wide single-nucleotide polymorphism dataset, we present a molecular phylogenetic reconstruction of genus Corylus (Betulaceae), which have a disjunct distribution between Eurasia and North America (NA). The aim is to explore the speciation patterns and evolutionary relationships of Corylus species by establishing a general phylogenetic framework with extensive sampling. Both the molecular phylogeny inferred from recombination-free dataset and structure analysis support the division of Corylus into four major clades (A-D). Recombination tests and hybridization detection reveal extensive recombination and hybridization events among different clades, which have potentially influenced the speciation process of Corylus. Divergence time estimation indicates that recent common ancestor (MRCA) of Corylus occurred in late Eocene (∼36.38 Ma) and subsequent rapid diversification began during Miocene. Ancestral area reconstruction shows that Corylus originated from southwest China. The arrival of two clades (Clades B and C) to NA was well supported by the long distance dispersal crossing the Bering land bridge. The Himalayas, European-Mediterranean area, and other distribution regions are primarily the recipients of dispersal taxa. Vicariance after dispersal plays an important role in speciation.
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comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus betulaceae species
Frontiers in Plant Science, 2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.
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Table_1_Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species.XLSX
2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.
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Table_1_Resolving the Speciation Patterns and Evolutionary History of the Intercontinental Disjunct Genus Corylus (Betulaceae) Using Genome-Wide SNPs.XLSX
2018Co-Authors: Zhen Yang, Lisong Liang, Tiantian Zhao, Guixi WangAbstract:Understanding the underlying mechanisms of species origin, divergence, and distribution patterns of the intercontinental disjunct taxa has long fascinated botanists. Based on 4,894 genome-wide single-nucleotide polymorphism dataset, we present a molecular phylogenetic reconstruction of genus Corylus (Betulaceae), which have a disjunct distribution between Eurasia and North America (NA). The aim is to explore the speciation patterns and evolutionary relationships of Corylus species by establishing a general phylogenetic framework with extensive sampling. Both the molecular phylogeny inferred from recombination-free dataset and structure analysis support the division of Corylus into four major clades (A–D). Recombination tests and hybridization detection reveal extensive recombination and hybridization events among different clades, which have potentially influenced the speciation process of Corylus. Divergence time estimation indicates that recent common ancestor (MRCA) of Corylus occurred in late Eocene (∼36.38 Ma) and subsequent rapid diversification began during Miocene. Ancestral area reconstruction shows that Corylus originated from southwest China. The arrival of two clades (Clades B and C) to NA was well supported by the long distance dispersal crossing the Bering land bridge. The Himalayas, European-Mediterranean area, and other distribution regions are primarily the recipients of dispersal taxa. Vicariance after dispersal plays an important role in speciation.
Paolo Boccacci - One of the best experts on this subject based on the ideXlab platform.
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in silico mining characterization and cross species transferability of est ssr markers for european hazelnut Corylus avellana l
Molecular Breeding, 2015Co-Authors: Shawn A. Mehlenbacher, Roberto Botta, Paolo Boccacci, Chiara Beltramo, M Sandoval A Prando, A Lembo, Chiara Sartor, Torello D MarinoniAbstract:The European hazelnut (Corylus avellana L.) is one of the most important nut crops. In this work, we characterize functional microsatellite or simple sequence repeat (SSR) markers for genetic analysis and molecular breeding in this species. A total of 38,454 Betulaceae EST sequences from NCBI resulted in 1,282 non-redundant EST-SSRs. Dinucleotide repeats were the most abundant (63.9 %), followed by trinucleotides (33.8 %). The putative functions of the non-redundant EST-SSRs were classified according to gene ontology (GO) categories (biological process, molecular function, and cellular component). A total of 921 sequences showed significant hits with the non-redundant protein database, and GO categories were assigned to 696 (75.5 %) of them. Flanking primer pairs were designed for 78 di- and trinucleotide EST-SSRs from Alnus glutinosa L. (29), Betula pendula Roth (26), and Betula platyphylla Suckaczev (23). Further, 41 dinucleotide repeats selected from hazelnut transcriptome sequences were added. Thirty-six out 119 primer pairs generated amplification products in six hazelnut accessions and in the samples of the species from which they were isolated. Among them, 20 were polymorphic when tested on 18 hazelnut cultivars. Fifteen loci are suitable for mapping in a F1 population of ‘Tonda Gentile delle Langhe’ × ‘Merveille de Bollwiller’ and 11 of them were functionally annotated. The cross-species transferability of 36 EST-SSR loci within nine Corylus species was also performed. The success rate of markers transferability (excluding C. avellana) ranged from 11 to 100 %, with an average of 55 %. The EST-SSRs developed increase the number of markers currently available for hazelnut.
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Characterization and evaluation of microsatellite loci in European hazelnut (Corylus avellana L.) and their transferability to other Corylus species
Molecular Ecology Notes, 2005Co-Authors: Paolo Boccacci, Shawn A. Mehlenbacher, Nahla V. Bassil, Aziz Akkak, Roberto BottaAbstract:In this work, 18 microsatellite loci were developed in the European hazelnut ( Corylus avellana L.) using three enriched genomic libraries. They were evaluated on a set of 20 accessions of this species on the basis of number of alleles (mean: 7.1), expected heterozygosity (mean: 0.67), power of discrimination (mean: 0.77) and polymorphism information content (mean: 0.64). Cross-species transferability was evaluated using seven other Corylus species. All primer pairs amplified in all species, except for CaT-C505 in Corylus ferox and CaT-A114 in Corylus californica .
Roberto Botta - One of the best experts on this subject based on the ideXlab platform.
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hazelnut Corylus spp breeding
2019Co-Authors: Roberto Botta, Veli Erdogan, Thomas J Molnar, Nadia Valentini, Daniela Torello Marinoni, Shawn A. MehlenbacherAbstract:Hazelnut is an economically important tree nut whose production is mostly destined to the confectionery industry with a demand that currently exceeds supply. Its cultivation remains substantially based on named selections from local, wild vegetation. Public breeding programs were not initiated until the 1960s and only two, both in the USA, are in operation today that are relatively large. Oregon State University has produced new cultivars with Gasaway resistance to the fungus Anisogramma anomala, causal agent of eastern filbert blight (EFB), a major disease in North America; these cultivars are being widely planted. In China, cold-hardy hybrid cultivars from Corylus heterophylla and C. avellana were recently released and are planted in northeastern China. In the past 25 years, molecular markers have facilitated a much better understanding of genetic diversity in the genus Corylus, aided the construction of linkage maps and allowed for marker-assisted selection for disease resistance. The genome of C. avellana was sequenced and assembled, and DNA markers identified from the transcriptome, providing the basis for the isolation of important genes, including those related to nut quality and adaptive and phenological traits. Many new genotypes expressing eastern filbert blight (EFB) resistance have been identified in the germplasm, and subsequent linked DNA markers developed, allowing new approaches to breeding for durable resistance. Micropropagation is routinely used in the USA, Chile and Italy for multiplication, but work with other in vitro techniques is less advanced. Genetic engineering has not been developed in hazelnut due to regeneration difficulties from somatic tissues but recent advances have established a protocol for organogenesis. More research is being carried out to assemble a high-quality hazelnut genome and achieve somatic embryogenesis. The results from this research will provide knowledge and tools enabling the isolation of genes and molecular markers, and the application of genome editing techniques to hazelnut.
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in silico mining characterization and cross species transferability of est ssr markers for european hazelnut Corylus avellana l
Molecular Breeding, 2015Co-Authors: Shawn A. Mehlenbacher, Roberto Botta, Paolo Boccacci, Chiara Beltramo, M Sandoval A Prando, A Lembo, Chiara Sartor, Torello D MarinoniAbstract:The European hazelnut (Corylus avellana L.) is one of the most important nut crops. In this work, we characterize functional microsatellite or simple sequence repeat (SSR) markers for genetic analysis and molecular breeding in this species. A total of 38,454 Betulaceae EST sequences from NCBI resulted in 1,282 non-redundant EST-SSRs. Dinucleotide repeats were the most abundant (63.9 %), followed by trinucleotides (33.8 %). The putative functions of the non-redundant EST-SSRs were classified according to gene ontology (GO) categories (biological process, molecular function, and cellular component). A total of 921 sequences showed significant hits with the non-redundant protein database, and GO categories were assigned to 696 (75.5 %) of them. Flanking primer pairs were designed for 78 di- and trinucleotide EST-SSRs from Alnus glutinosa L. (29), Betula pendula Roth (26), and Betula platyphylla Suckaczev (23). Further, 41 dinucleotide repeats selected from hazelnut transcriptome sequences were added. Thirty-six out 119 primer pairs generated amplification products in six hazelnut accessions and in the samples of the species from which they were isolated. Among them, 20 were polymorphic when tested on 18 hazelnut cultivars. Fifteen loci are suitable for mapping in a F1 population of ‘Tonda Gentile delle Langhe’ × ‘Merveille de Bollwiller’ and 11 of them were functionally annotated. The cross-species transferability of 36 EST-SSR loci within nine Corylus species was also performed. The success rate of markers transferability (excluding C. avellana) ranged from 11 to 100 %, with an average of 55 %. The EST-SSRs developed increase the number of markers currently available for hazelnut.
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Characterization and evaluation of microsatellite loci in European hazelnut (Corylus avellana L.) and their transferability to other Corylus species
Molecular Ecology Notes, 2005Co-Authors: Paolo Boccacci, Shawn A. Mehlenbacher, Nahla V. Bassil, Aziz Akkak, Roberto BottaAbstract:In this work, 18 microsatellite loci were developed in the European hazelnut ( Corylus avellana L.) using three enriched genomic libraries. They were evaluated on a set of 20 accessions of this species on the basis of number of alleles (mean: 7.1), expected heterozygosity (mean: 0.67), power of discrimination (mean: 0.77) and polymorphism information content (mean: 0.64). Cross-species transferability was evaluated using seven other Corylus species. All primer pairs amplified in all species, except for CaT-C505 in Corylus ferox and CaT-A114 in Corylus californica .
