Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research

@article{Strijk2019TrochodendronAT,
  title={Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research},
  author={Joeri Sergej Strijk and Damien Daniel Hinsinger and Fengqiao Zhang and Kunfang Cao},
  journal={GigaScience},
  year={2019},
  volume={8}
}
Background The wheel tree (Trochodendron aralioides) is one of only two species in the basal eudicot order Trochodendrales. Together with Tetracentron sinense, the family is unique in having secondary xylem without vessel elements, long considered to be a primitive character also found in Amborella and Winteraceae. Recent studies however have shown that Trochodendraceae belong to basal eudicots and demonstrate this represents an evolutionary reversal for the group. Trochodendron aralioides is… 

A chromosome‐level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae)

Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

A high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales) is presented and it is revealed that Buxales and Trochodendrales are genetically similar and classified as sisters, which reveals the likely relationships and evolutionary histories of early eudicots.

Chromosome‐level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology

The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages.

The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding

A chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive.

The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa

The assembled nuclear, mitochondrial and chloroplast genomes provide a significant source of genetic data for further works on phylogeny, hybridisation and population studies within Stipa and the grass family Poaceae.

Buxus and Tetracentron genomes help resolve eudicot genome history

It is shown that Buxus and Tetracentron are both characterized by independent WGDs, resolve relationships among early-diverging eudicots and their respective genomes, and the RACCROCHE pipeline is used to reconstruct ancestral genome structure at three key phylogenetic nodes of eudicot diversification.

A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

A chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany), adds to the available highly resolved plant genomes and is hoped to serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.

Single-cell transcriptomics unveils xylem cell development and evolution

This evo-devo framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history.

Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome level scaffolds suitable for comparative genomic analyses.

References

SHOWING 1-10 OF 71 REFERENCES

First nuclear DNA C-values for 28 angiosperm genera.

Overall familial representation for genome size for angiosperms may prove impossible in any short period, and progress towards this goal will become slower as unrepresented families will become increasingly enriched for monotypic taxa from obscure locations that are harder to access.

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses.

OrthoMCL: identification of ortholog groups for eukaryotic genomes.

OrthoMCL provides a scalable method for constructing orthologous groups across multiple eukaryotic taxa, using a Markov Cluster algorithm to group (putative) orthologs and paralogs.

Phased diploid genome assembly with single-molecule real-time sequencing

The open-source FALCON and FALcon-Unzip algorithms are introduced to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes.

PAML 4: phylogenetic analysis by maximum likelihood.

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

It is demonstrated that fragScaff is complementary to Hi-C-based contact probability maps, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

This study reports a computational method, CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data, and defines a set of conserved protein families that occur in a wide range of eukaryotes and presents a mapping procedure that accurately identifies their exon-intron structures in a novel genomic sequence.

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

A computerized method is presented that reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
...