Abstract:Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast gen… Show more
“…The present results are similar to the chloroplast genomes of A . s i nens i s
46 and species within the genus Ulmus
49 in terms of codon usage.Figure 4Codon content of 20 amino acid and stop codons in all protein-coding genes of the chloroplast genomes of two species. The histogram on the left-hand side of each amino acid shows codon usage within the T .…”
Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively. Compared with the chloroplast genomes of Nicotiana tabacum and Osyris alba, all ndh genes as well as three ribosomal protein genes, seven tRNA genes, four ycf genes, and the infA gene of these two species have been lost. The results of the maximum likelihood and neighbor-joining phylogenetic trees strongly support the theory that Loranthaceae and Viscaceae are monophyletic clades. This research reveals the effect of a parasitic lifestyle on the chloroplast structure and genome content of T. chinensis and T. sutchuenensis, and enhances our understanding of the discrepancies in terms of assembly results between Illumina and PacBio.
“…The present results are similar to the chloroplast genomes of A . s i nens i s
46 and species within the genus Ulmus
49 in terms of codon usage.Figure 4Codon content of 20 amino acid and stop codons in all protein-coding genes of the chloroplast genomes of two species. The histogram on the left-hand side of each amino acid shows codon usage within the T .…”
Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively. Compared with the chloroplast genomes of Nicotiana tabacum and Osyris alba, all ndh genes as well as three ribosomal protein genes, seven tRNA genes, four ycf genes, and the infA gene of these two species have been lost. The results of the maximum likelihood and neighbor-joining phylogenetic trees strongly support the theory that Loranthaceae and Viscaceae are monophyletic clades. This research reveals the effect of a parasitic lifestyle on the chloroplast structure and genome content of T. chinensis and T. sutchuenensis, and enhances our understanding of the discrepancies in terms of assembly results between Illumina and PacBio.
“…In the first complete chloroplast genomic sequencing study of the Ulmaceae, the genus Ulmus appears to be close, in order of distance, to Cannabaceae, Moraceae, Rosaceae, Juglandaceae and Salicaceae (Zuo et al., ). Ulmus contains 20–45 species, mostly north temperate, concentrated in Eurasia and the mountains of tropical Asia; three species extend into the tropics (Caudullo & de Rigo, ; Richens, ).…”
This account presents information on all aspects of the biology of Ulmus glabraHudson (wych elm) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of the British Isles: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history and conservation.2. Ulmus glabra is a large forest tree, and often an important canopy tree in ancient and semi-natural woodlands. It is primarily native to the north and west of Britain and much of mainland Europe. It is the only elm native to Ireland. It is the most distinct of the British elms in that it rarely suckers and sets abundant viable seed.Although found on limestone screes and cliffs, and hedgerows, it is primarily a woodland tree, especially on moist, basic soils. In many secondary woodlands, it often co-occurs with Acer pseudoplatanus and has ecological needs that are similar to Fraxinus excelsior.
3.Ulmus glabra has clusters of c. 25 hermaphrodite flowers appearing before the leaves on previous year's growth. Seeds are wind-dispersed, falling in April to July, but remain viable for only a few days. Nevertheless, seedling establishment can be abundant. Hybridisation with other northern European elms is common but hybrids are notoriously difficult to identify and therefore probably under-recorded.4. The health and survival of wych elm in Europe has been seriously compromised since the 1970s due to Dutch elm disease caused by the fungus Ophiostoma novoulmi, transmitted by elm bark beetles (Scolytus spp.). To the south of its Scottish stronghold, many elms are reduced to small trees regrowing from basal sprouts or seeds. These trees tend to be reinfected once trunk diameter exceeds 10 cm.Fortunately for its long-term survival, seed production usually begins a number of years before they are reinfected.
“…We evaluated the chloroplast genomes of the eight Ulmus species, two species closely related to Ulmus ( M. mongolica and C. sativa ), and A. thaliana for the presence and absence of particular genes (Table 4). Five genes ( pet B , pet D , psb L , rps 16, and trn K) were present in American elm but absent from all Asian elms (Zuo et al, 2017;Zhang et al, 2019a;Zhang et al, 2019b). The gene ycf 15 was present in all elms but absent from the related species Morus mongolica , Cannibis sativa , and Arabidopsis thaliana .…”
Section: Resultsmentioning
confidence: 98%
“…The chloroplast genomes were assembled with BWA (Burrows Wheeler-aligner), Picard-tools and GATK (Genome Analysis Toolkit) software (Langmead et al, 2009;McKenna et al, 2010;Wysoker et al, 2019). The U. davidiana (NC_032718.1) genome (Zuo et al, 2017) was used as a preliminary reference to guide assembly of the RV16 genotype, and subsequently the RV16 assembly was used to fill gaps of the Am. 57845 genotype.…”
Section: Methodsmentioning
confidence: 99%
“…These include: U. pumila ., U. laciniata , U. davidiana , U. macrocarpa , U. davidiana var. japonica (Zuo et al, 2017), U. gaussenii (Zhang et al, 2019a), and U. chenmoui (Zhang et al, 2019b). However, the genomes of North American elms, including the most important North American species, U. americana , are not yet published.…”
American elm, Ulmus americana L., was cultivated widely in USA and Canada as a landscape tree, but the genome of this important species is poorly characterized. For the first time, we describe the sequencing and assembly of the chloroplast genomes of two American elm genotypes (RV16 and Am57845). The complete chloroplast genome of U. americana ranged from 158,935-158,993 bp. The genome contains 127 genes, including 85 protein-coding genes, 34 tRNA genes and 8 rRNA genes. Between the two American elm chloroplasts we sequenced, we identified 240 sequence variants (SNPs and indels). To evaluate the phylogeny of American elm, we compared the chloroplast genomes of two American elms along with seven Asian elm species and twelve other chloroplast genomes available through the NCBI database. As expected, Ulmus was closely related to Morus and Cannabis, as all three genera are assigned to the Urticales. Comparison of American elm with Asian elms revealed that trnH was absent from the chloroplast of American elm but not most Asian elms; conversely, petB, petD, psbL, trnK, and rps16 are present in the American elm but absent from all Asian elms. The complete chloroplast genome of U. americana will provide useful genetic resources for characterizing the genetic diversity of U. americana and potentially help to conserve natural populations of American elm.
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