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

  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 Feng-Ping Zhang and Kun-fang Cao},
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… Expand
Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
The T. aralioides genome is the first chromosome-scale genome assembled in the order Trochodendrales and represents the largest genome assembled to date in the basal eudicot grade, as well as the closest order relative to the core-eudicots, as the position of Buxales remains unresolved. Expand
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.Expand
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation and population genomics reveals its genetic diversity and geographic structure with implications for conservation. Expand
Chromosome‐level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology
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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. Expand
A chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs
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This evo-developmental 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. Expand
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. Expand


The Evolution of Angiosperm Trees: From Palaeobotany to Genomics
Genomic resources for angiosperm trees are developing rapidly and this, coupled with the huge variation in woody habit, make angiosperms a highly promising comparative system for understanding wood evolution at the molecular level. Expand
Newly Recognized Diversity in Trochodendraceae from the Eocene of Western North America
Using microcomputed tomography (μCT) scanning to augment traditional methods, additional diversity is recognized, including two new fruit types of Concavistylon wehrii and Pentacentron, indicating that the Trochodendraceae family was more diverse 50–52 Ma than it is today. Expand
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. Expand
Trochodendraceous Fruits and Foliage in the Miocene of Western North America
Abstract Two fossil fruit types and at least one fossil leaf type representing Trochodendraceae are recognized from the middle Miocene Cascadia flora of western Oregon, USA. Trochodendron rosayi sp.Expand
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. Expand
Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches, and enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences. Expand
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. Expand
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. Expand
PAML 4: phylogenetic analysis by maximum likelihood.
  • Ziheng Yang
  • Medicine, Biology
  • Molecular biology and evolution
  • 2007
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. Expand
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. Expand