Next-generation sequencing (NGS) technologies are a powerful new tool for conducting studies in ecology and evolutionary biology. NGS offers the possibility of genetic characterisation of many loci ...in non-model organisms, opening up a plethora of research opportunities unimaginable 10 years ago. This was the motivation behind a discussion meeting entitled Next generation plant ecology and evolution, held at the Royal Botanic Garden Edinburgh in October 2011. This special feature includes a series of papers presented at the meeting. These studies demonstrate the wide range of areas on which the use of NGS can shed light, ranging from the characterisation of single loci to whole genomes.
Recently diverged species often show incomplete reproductive isolation and subsequently experience hybridization and introgression. The plant genus Mimulus includes many such examples of closely ...related taxa that prove useful for studying incipient speciation. However, Sandstedt et al. show that in contrast to other Mimulus species, species of the M. tilingii complex are characterized by strong postzygotic isolation mediated by multiple barriers. This finding highlights the diverse speciation histories of related plant groups.
PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and ...contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing.
MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats.
MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).
We present a genome assembly of an
Arabidopsis thaliana
specimen (thale cress; Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence spans 138 megabases. Most of the assembly ...(98.76%) is scaffolded into five chromosomal pseudomolecules. The mitochondrial and plastid genomes were also assembled and are 368.8 and 154.5 kilobases in length respectively.
Homeobox genes encode transcription factors with essential roles in patterning and cell fate in developing animal embryos. Many homeobox genes, including Hox and NK genes, are arranged in gene ...clusters, a feature likely related to transcriptional control. Sparse taxon sampling and fragmentary genome assemblies mean that little is known about the dynamics of homeobox gene evolution across Lepidoptera or about how changes in homeobox gene number and organization relate to diversity in this large order of insects. Here we analyze an extensive data set of high-quality genomes to characterize the number and organization of all homeobox genes in 123 species of Lepidoptera from 23 taxonomic families. We find most Lepidoptera have around 100 homeobox loci, including an unusual Hox gene cluster in which the
gene is repositioned and the
gene is next to
A topologically associating domain spans much of the gene cluster, suggesting deep regulatory conservation of the Hox cluster arrangement in this insect order. Most Lepidoptera have four Shx genes, divergent
-derived loci, but these loci underwent dramatic duplication in several lineages, with some moths having over 165 homeobox loci in the Hox gene cluster; this expansion is associated with local LINE element density. In contrast, the NK gene cluster content is more stable, although there are differences in organization compared with other insects, as well as major rearrangements within butterflies. Our analysis represents the first description of homeobox gene content across the order Lepidoptera, exemplifying the potential of newly generated genome assemblies for understanding genome and gene family evolution.
Abstract
A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In
Begonia
, one of the largest plant genera (1900+ species), it has been postulated that the ...high number of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in
Begonia
by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between
B. heracleifolia
and
B. nelumbiifolia
are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between
B. heracleifolia
and
B. sericoneura
contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that
Begonia
demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.
Telling plant species apart with DNA: from barcodes to genomes Hollingsworth, Peter M.; Li, De-Zhu; van der Bank, Michelle ...
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
09/2016, Letnik:
371, Številka:
1702
Journal Article
Recenzirano
Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity—yet many tens of thousands of species ...await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets. This article is part of the themed issue 'From DNA barcodes to biomes'.
Begonia is one of the ten largest angiosperm genera with over 1,500 species found throughout the tropics. To use this group as a model for the evolution of diversity in tropical herbaceous plants, we ...have produced three species transcriptomes, physical genome size measures, and two backcross genetic maps. We chose to focus on two Central American species, B. conchifolia and B. plebeja, and one SE Asian species, B. venusta, allowing us to pose questions at widely different evolutionary scales within the genus. We used next generation sequencing of cDNA libraries to produce annotated transcriptome databases for each of the three species. Though Begonia is functionally diploid, transcriptome analysis suggested a genome duplication occurred at or near the base of the Begonia clade. The genetic maps were built from first generation backcrosses in both directions between B. plebeja and B.conchifolia using 105 SNP markers in genes known to regulate development that were identified from the transcriptomes and the map bulked out with 226 AFLP loci. The genetic maps had 14 distinct linkage groups each and mean marker densities of between 3.6 and 5.8 cM providing between 96 and 99 % genomic coverage within 10 cM. We measured genome size 1C value of 0.60 and 0.63 pg for B. conchifolia and B. plebeja corresponding to recombination rates of between 441 and 451 Kb per cM in the genetic maps. Altogether, these new data represent a powerful new set of molecular genetic tools for evolutionary study in the genus Begonia.
Abstract
Species delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, ...phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine
Cassytha filiformis
(Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well‐supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil‐calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo‐Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of
C. filiformis
. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones.
PDF
