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Article: Target capture sequencing unravels Rubus evolution

Carter, Katie A / Liston, Aaron / Bassil, Nahla V / Lawrence A. Alice / Bushakra, Jill M / Sutherland, Brittany L / Mockler, Todd C / Bryant, Douglas W / Hummer, Kim E

Frontiers in plant science. , v. 10

2019

Abstract: Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently ... ...

Abstract	Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.
Keywords	Miocene epoch ; Rubus ; ancestry ; biogeography ; birds ; blackberries ; computer software ; cultivars ; data collection ; estimation ; genes ; hybridization ; hybrids ; land ; monophyly ; nucleotide sequences ; objectives ; ploidy ; polyphyly ; raspberries ; research ; sorting ; species diversity ; taxonomy ; Arctic region ; Asia ; Europe ; North America ; Pacific Ocean Islands ; South America
Language	English
Dates of publication	2019-1220
Document type	Article
Note	NAL-light
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2019.01615
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Detection and quantification of alternative splicing variants using RNA-seq.

Bryant, Douglas W / Priest, Henry D / Mockler, Todd C

Methods in molecular biology (Clifton, N.J.)

2012 Volume 883, Page(s) 97–110

Abstract: Next-generation sequencing has enabled genome-wide studies of alternative pre-mRNA splicing, allowing for empirical determination, characterization, and quantification of the expressed RNAs in a sample in toto. As a result, RNA sequencing (RNA-seq) has ... ...

Abstract	Next-generation sequencing has enabled genome-wide studies of alternative pre-mRNA splicing, allowing for empirical determination, characterization, and quantification of the expressed RNAs in a sample in toto. As a result, RNA sequencing (RNA-seq) has shown tremendous power to drive biological discoveries. At the same time, RNA-seq has created novel challenges that necessitate the development of increasingly sophisticated computational approaches and bioinformatic tools. In addition to the analysis of massive datasets, these tools also need to facilitate questions and analytical approaches driven by such rich data. HTS and RNA-seq are still in a stage of very rapid evolution and are, therefore, only introduced in general terms. This chapter mainly focuses on the methods for discovery, detection, and quantification of alternatively spliced transcript variants.
MeSH term(s)	Alternative Splicing ; Contig Mapping/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; RNA, Messenger/genetics ; RNA, Messenger/isolation & purification ; Sequence Alignment/methods ; Sequence Analysis, RNA/methods ; Software
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2012
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-839-9_7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Target Capture Sequencing Unravels

Carter, Katherine A / Liston, Aaron / Bassil, Nahla V / Alice, Lawrence A / Bushakra, Jill M / Sutherland, Brittany L / Mockler, Todd C / Bryant, Douglas W / Hummer, Kim E

Frontiers in plant science

2019 Volume 10, Page(s) 1615

Abstract: ... ...

Abstract	Rubus
Language	English
Publishing date	2019-12-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2019.01615
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: QSRA: a quality-value guided de novo short read assembler.

Bryant, Douglas W / Wong, Weng-Keen / Mockler, Todd C

BMC bioinformatics

2009 Volume 10, Page(s) 69

Abstract: Background: New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for ...

Abstract	Background: New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data. Results: We have designed and implemented an assembler, Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality. Conclusion: QSRA generally produced the highest genomic coverage, while being faster than VCAKE. QSRA is extremely competitive in its longest contig and N50/N80 contig lengths, producing results of similar quality to those of EDENA and VELVET. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE algorithm by not only drastically reducing runtimes but also increasing the viability of the assembly algorithm through further error handling capabilities.
MeSH term(s)	Algorithms ; Computational Biology/methods ; Programming Languages ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2009-02-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-10-69
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Article ; Online: QSRA – a quality-value guided de novo short read assembler

Mockler Todd C / Wong Weng-Keen / Bryant Douglas W

BMC Bioinformatics, Vol 10, Iss 1, p

2009 Volume 69

Abstract: Abstract Background New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to ... ...

Abstract	Abstract Background New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data. Results We have designed and implemented an assembler, Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality. Conclusion QSRA generally produced the highest genomic coverage, while being faster than VCAKE. QSRA is extremely competitive in its longest contig and N50/N80 contig lengths, producing results of similar quality to those of EDENA and VELVET. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE algorithm by not only drastically reducing runtimes but also increasing the viability of the assembly algorithm through further error handling capabilities.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2009-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Characterization of aphid resistance loci in black raspberry (Rubus occidentalis L.)

Bushakra, JillM / Bassil, NahlaV / Bryant, DouglasW / Carter, KatherineA / Dossett, Michael / Finn, ChadE / Lee, JanaC / Lee, Jungmin / Mockler, ToddC / VanBuren, Robert / Vining, KellyJ

Molecular breeding. 2018 July, v. 38, no. 7

2018

Abstract: Viruses vectored by the aphid Amphorophora agathonica cause decline in black raspberry plant health resulting in a shortened life and poor fruit quality of the infected plantings. New aphid resistant cultivars could increase the longevity of plantings ... ...

Abstract	Viruses vectored by the aphid Amphorophora agathonica cause decline in black raspberry plant health resulting in a shortened life and poor fruit quality of the infected plantings. New aphid resistant cultivars could increase the longevity of plantings providing growers and processors with consistent fruit production. Recent exploration of the native range of black raspberry identified three sources of aphid resistance: Ag 4 from Ontario (ON), Canada, Ag 5 from Maine (ME), and a third source from Michigan (MI) with no formal designation. The objectives of this study were to assess segregation of these three sources of aphid resistance in populations with single and combined sources and develop markers that can identify each source of resistance. A genetic linkage map constructed for ORUS 4305 placed the ON aphid resistance locus on Rubus linkage group (RLG) 6. Segregation ratios in populations with single and combined sources, and linkage mapping in two populations (ORUS 4304 and ORUS 4812) segregating for the Ag 5 and MI sources, respectively, indicated that these three sources of resistance are each conferred by single dominant genes/alleles that are linked on RLG6. Confirmation of marker association in 16 validation populations identified four markers that could be used to predict resistance; however, none could distinguish between the ON and MI sources. These four markers may be useful for screening populations to enrich the field-planted progeny for aphid resistance. Fine mapping of the resistance loci is needed to develop functional markers at each of the resistance loci to enable pyramiding and durable aphid resistance.
Keywords	alleles ; Amphorophora agathonica ; biomarkers ; chromosome mapping ; cultivars ; dominant genes ; fruits ; linkage groups ; loci ; longevity ; plant health ; progeny ; Rubus occidentalis ; screening ; viruses ; Maine ; Michigan ; Ontario
Language	English
Dates of publication	2018-07
Size	p. 83.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	1230924-2
ISSN	1572-9788 ; 1380-3743
ISSN (online)	1572-9788
ISSN	1380-3743
DOI	10.1007/s11032-018-0839-5
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Exploring the switchgrass transcriptome using second-generation sequencing technology.

Wang, Yixing / Zeng, Xin / Iyer, Niranjani J / Bryant, Douglas W / Mockler, Todd C / Mahalingam, Ramamurthy

PloS one

2012 Volume 7, Issue 3, Page(s) e34225

Abstract: Background: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of ... ...

Abstract	Background: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of genomic resources for this plant is necessary. The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies. Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass. Principal findings: Switchgrass cDNA libraries from germinating seedlings, emerging tillers, flowers, and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology, generating 980,000 reads with an average read length of 367 bp. De novo assembly generated 243,600 contigs with an average length of 535 bp. Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs. Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium, sorghum, rice and maize indicated a 70-80% overlap. RPKM analysis demonstrated unique transcriptional signatures of the four tissues analyzed in this study. More than 24,000 ESTs were identified in the dormant seed library. In silico analysis indicated that there are more than 2000 EST-SSRs in this collection. Expression of several orphan ESTs was confirmed by RT-PCR. Significance: We estimate that about 90% of the switchgrass gene space has been covered in this analysis. This study nearly doubles the amount of EST information for switchgrass currently in the public domain. The celerity and economical nature of second-generation sequencing technologies provide an in-depth view of the gene space of complex genomes like switchgrass. Sequence analysis of closely related members of the NAD(+)-malic enzyme type C4 grasses such as the model system Setaria viridis can serve as a viable proxy for the switchgrass genome.
MeSH term(s)	Algorithms ; Computational Biology/methods ; DNA, Complementary/metabolism ; Expressed Sequence Tags ; Gene Expression Profiling ; Gene Library ; Genes, Plant ; Genetic Markers ; Genome, Plant ; Genomics ; Models, Genetic ; Molecular Sequence Annotation ; Photosynthesis ; Poaceae/genetics ; Polyploidy ; Sequence Analysis, DNA ; Software ; Transcription, Genetic ; Transcriptome
Chemical Substances	DNA, Complementary ; Genetic Markers
Language	English
Publishing date	2012-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0034225
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Supersplat--spliced RNA-seq alignment.

Bryant, Douglas W / Shen, Rongkun / Priest, Henry D / Wong, Weng-Keen / Mockler, Todd C

Bioinformatics (Oxford, England)

2010 Volume 26, Issue 12, Page(s) 1500–1505

Abstract: Motivation: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, ... ...

Abstract	Motivation: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data. Results: Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of approximately 11.4 million reads per hour. We further benchmark the performance of the algorithm by mapping Illumina RNA-seq reads to identify introns in the genome of the reference dicot plant Arabidopsis thaliana and we demonstrate the utility of supersplat for de novo empirical annotation of splice junctions using the reference monocot plant Brachypodium distachyon. Availability: Implemented in C++, supersplat source code and binaries are freely available on the web at http://mocklerlab-tools.cgrb.oregonstate.edu/.
MeSH term(s)	Base Sequence ; Genomics/methods ; RNA Splicing ; Sequence Alignment/methods ; Sequence Analysis, RNA/methods ; Software
Language	English
Publishing date	2010-04-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btq206
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Article ; Online: A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica.

Bushakra, Jill M / Bryant, Douglas W / Dossett, Michael / Vining, Kelly J / VanBuren, Robert / Gilmore, Barbara S / Lee, Jungmin / Mockler, Todd C / Finn, Chad E / Bassil, Nahla V

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

2015 Volume 128, Issue 8, Page(s) 1631–1646

Abstract: Key message: We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North ... ...

Abstract	Key message: We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3-4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.
MeSH term(s)	Animals ; Aphids ; Breeding ; Chromosome Mapping ; Chromosomes, Plant ; DNA, Plant/genetics ; Genetic Linkage ; Genetic Markers ; Genetics, Population ; Herbivory ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; Rubus/genetics
Chemical Substances	DNA, Plant ; Genetic Markers
Language	English
Publishing date	2015-08
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2170-2
ISSN	1432-2242 ; 0040-5752
ISSN (online)	1432-2242
ISSN	0040-5752
DOI	10.1007/s00122-015-2541-x
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Article ; Online: A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag 4 conferring resistance to the aphid Amphorophora agathonica

Bushakra, Jill M. / Bryant, Douglas W. / Dossett, Michael / Vining, Kelly J. / VanBuren, Robert / Gilmore, Barbara S. / Lee, Jungmin / Mockler, Todd C. / Finn, Chad E. / Bassil, Nahla V.

Theor Appl Genet. 2015 Aug., v. 128, no. 8 p.1631-1646

2015

Abstract: KEY MESSAGE : We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North ... ...

Abstract	KEY MESSAGE : We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3–4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F₁ population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.
Keywords	Amphorophora agathonica ; Rubus occidentalis ; chromosome mapping ; cultivars ; genetic variation ; genome assembly ; germplasm ; haploidy ; loci ; markets ; microsatellite repeats ; plant health ; progeny ; raspberries ; single nucleotide polymorphism ; viruses ; North America
Language	English
Dates of publication	2015-08
Size	p. 1631-1646.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
Note	Resource is Open Access
ZDB-ID	2170-2
ISSN	1432-2242 ; 0040-5752
ISSN (online)	1432-2242
ISSN	0040-5752
DOI	10.1007/s00122-015-2541-x
Database	NAL-Catalogue (AGRICOLA)

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