Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

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Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

BMC Ecology and Evolution ◽

10.1186/s12862-021-01751-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

J. S. Eriksson ◽

C. D. Bacon ◽

D. J. Bennett ◽

B. E. Pfeil ◽

B. Oxelman ◽

...

Keyword(s):

Chromosome Number ◽

Chromosome Numbers ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Single Copy ◽

Target Sequence ◽

Whole Genome ◽

Genome Doubling ◽

Sequence Capture ◽

Duplication Events

Abstract Background The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

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Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

10.21203/rs.3.rs-48002/v4 ◽

2021 ◽

Author(s):

Jonna Sofia Eriksson ◽

Christine D. Bacon ◽

Dominic J. Bennett ◽

Bernard E. Pfeil ◽

Bengt Oxelman ◽

...

Keyword(s):

Chromosome Number ◽

Chromosome Numbers ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Single Copy ◽

Target Sequence ◽

Whole Genome ◽

Genome Doubling ◽

Sequence Capture ◽

Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

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Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

American Journal of Botany ◽

10.1002/ajb2.1678 ◽

2021 ◽

Author(s):

Anne E. Thomas ◽

Javier Igea ◽

Heidi M. Meudt ◽

Dirk C. Albach ◽

William G. Lee ◽

...

Keyword(s):

New Zealand ◽

Target Sequence ◽

Rapid Radiation ◽

Sequence Capture ◽

Phylogenetic Resolution

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A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

10.1101/2021.02.22.431589 ◽

2021 ◽

Author(s):

William J. Baker ◽

Paul Bailey ◽

Vanessa Barber ◽

Abigail Barker ◽

Sidonie Bellot ◽

...

Keyword(s):

Natural History ◽

Flowering Plants ◽

Tree Of Life ◽

Flowering Plant ◽

Target Sequence ◽

Sequence Capture ◽

Natural History Collections ◽

Public Data ◽

Data Release ◽

Life On Earth

AbstractThe tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a “first pass” angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections.

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More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

Biology Letters ◽

10.1098/rsbl.2012.0331 ◽

2012 ◽

Vol 8 (5) ◽

pp. 783-786 ◽

Cited By ~ 233

Author(s):

Nicholas G. Crawford ◽

Brant C. Faircloth ◽

John E. McCormack ◽

Robb T. Brumfield ◽

Kevin Winker ◽

...

Keyword(s):

High Throughput Sequencing ◽

Common Ancestor ◽

Sister Group ◽

Single Copy ◽

Recent Analysis ◽

Phylogenetic Position ◽

Ultraconserved Elements ◽

Sequence Capture ◽

Genomic Scale ◽

Nuclear Loci

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To test this hypothesis with data from many single-copy nuclear loci dispersed throughout the genome, we used sequence capture, high-throughput sequencing and published genomes to obtain sequences from 1145 ultraconserved elements (UCEs) and their variable flanking DNA. The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.

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Detection of avian oncogenic Marek’s disease herpesvirus DNA in human sera

Journal of General Virology ◽

10.1099/0022-1317-82-1-233 ◽

2001 ◽

Vol 82 (1) ◽

pp. 233-240 ◽

Cited By ~ 9

Author(s):

S. Laurent ◽

E. Esnault ◽

G. Dambrine ◽

A. Goudeau ◽

D. Choudat ◽

...

Keyword(s):

Nested Pcr ◽

Hot Spot ◽

Health Hazard ◽

Single Copy ◽

Marek's Disease ◽

Target Sequence ◽

Marek’S Disease ◽

Serum Samples ◽

Worldwide Distribution ◽

Human Sera

The avian herpesvirus Marek’s disease virus (MDV) has a worldwide distribution and is responsible for T-lymphoma in chickens. The question as to whether MDV poses a public health hazard to humans was first raised when the virus was isolated in 1967. However, no irrefutable results have been obtained in immunological and virological studies. We used a nested-PCR to detect MDV DNA in human serum samples. A total of 202 serum samples from individuals exposed and not exposed to poultry was tested by nested-PCR for a target sequence located in the MDV gD gene. The assay system was specific and sensitive, making it possible to detect a single copy of the target sequence. Forty-one (20%) of the 202 serum samples tested positive for MDV DNA. The prevalence of MDV DNA was not significantly different in the group exposed to poultry and the group not exposed to poultry. There was also no difference due to age or sex. Alignment of the 41 gD sequences amplified from human sera with eight gD sequences amplified from MDV-infected chicken sera showed a maximum nucleotide divergence of 1·65%. However, four ‘hot-spot’ mutation sites were identified, defining four groups. Interestingly, two groups contained only human MDV-gD sequences. The status of the MDV genome detected in human blood is discussed.

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