scholarly journals Comparative whole plastome and low copy number phylogenetics of the core Saccharinae and Sorghinae.

2022 ◽  
Author(s):  
Dyfed Lloyd Evans ◽  
Ben Hughes ◽  
Shailesh Vinay Joshi
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
New World ◽  
Genetic Resource ◽  
Phylogenetic Analyses ◽  
World Species ◽  
Separate Genus ◽  
The Core ◽  
Low Copy Number ◽  
Long Read

Despite over 60 years' worth of taxonomic efforts, the relationships between sugarcane (Saccharum hybrid cultivars), Sorghum and their closest evolutionary relatives remain largely unresolved. Even relationships between generally accepted genera such as Miscanthus and Saccharum have not been examined in any large-scale molecular detail. Genera such as Erianthus, Miscanthidium and Narenga pose even greater taxonomic contention. Erianthus is not monophyletic and Erianthus sect. Ripidium (Valdés and Scholz 2006, Lloyd Evans et al. 2019a; Welker et al. 2019) represents a distinct and separate genus, Tripidium Scholz. Miscanthidium is placed within Miscanthus by many workers, whilst the New World Erianthus species and Narenga are currently placed within Saccharum. As these species represent a significant portion of the gene pool that sugarcane breeders use for introgression into sugarcane, their taxonomic placement and relationships to Saccharum are of significant economic import. Erianthus species from the Americas have not been significantly employed in sugarcane breeding and may represent an untapped genetic resource. In an attempt to resolve the taxonomic relationships of these genera, we have assembled three novel chloroplasts, from Miscanthidium capense, Miscanthidium junceum and Narenga porphyrocoma (this latter assembled from transcriptomic and long read data). In parallel, five low copy number loci have been assembled from species within Saccharum, Miscanthus, Sarga and Sorghum. Phylogenetic analyses were performed using both low copy number genes and whole chloroplasts. The phylogenetic results were compared with karyotype data to circumscribe the genera most closely related to sugarcane. We reveal that genera Miscanthus and Saccharum are monophyletic and have never undergone polyploidization outside their own genera. Genera Erianthus, Miscanthidium and Narenga are allopolyploids, which excludes them from being members of Saccharum and Miscanthus. Moreover, all three of these genera have divergent evolutionary histories. We therefore support the use of the genera Miscanthus, Miscanthidium, Erianthus (for the New World Species) and Narenga for those species and genera most closely allied to Saccharum. Our data demonstrate that all these genera should be excluded from Saccharum sensu lato.

scholarly journals Multiple Displacement Amplification as a Solution for Low Copy Number Plasmid Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Kuan Yao ◽  
Narjol González-Escalona ◽  
Maria Hoffmann
Keyword(s):  
Antibiotic Resistance ◽  
Single Molecule ◽  
Plasmid Dna ◽  
Copy Number ◽  
Sequence Data ◽  
Multiple Displacement Amplification ◽  
Fast Method ◽  
Alkaline Lysis ◽  
Low Copy Number ◽  
Long Read

Plasmids play a major role in bacterial adaptation to environmental stress and often contribute to antibiotic resistance and disease virulence. Although the complete sequence of each plasmid is essential for studying plasmid biology, most antibiotic resistance and virulence plasmids in Salmonella are present only in a low copy number, making extraction and sequencing difficult. Long read sequencing technologies require higher concentrations of DNA to provide optimal results. To resolve this problem, we assessed the sufficiency of multiple displacement amplification (MDA) for replicating Salmonella plasmid DNA to a satisfactory concentration for accurate sequencing and multiplexing. Nine Salmonella enterica isolates, representing nine different serovars carrying plasmids for which sequence data are already available at NCBI, were cultured and their plasmids isolated using an alkaline lysis extraction protocol. We then used the Phi29 polymerase to perform MDA, thereby obtaining enough plasmid DNA for long read sequencing. These amplified plasmids were multiplexed and sequenced on one single molecule, real-time (SMRT) cell with the Pacific Biosciences (Pacbio) Sequel sequencer. We were able to close all Salmonella plasmids (sizes ranged from 38 to 166 Kb) with sequencing coverage from 24 to 2,582X. This protocol, consisting of plasmid isolation, MDA, and multiplex sequencing, is an effective and fast method for closing high-molecular weight and low-copy-number plasmids. This high throughput protocol reduces the time and cost of plasmid closure.

Review of the New World species of Microplitis Foerster (Hymenoptera, Braconidae, Microgastrinae) attacking Sphingidae (Lepidoptera, Bombycoidea)

2021 ◽  
pp. 1-21
Author(s):  
Mostafa Ghafouri Moghaddam ◽  
Sloan Tomlinson ◽  
Samuel Jaffe ◽  
Diana Carolina Arias-Penna ◽  
James B. Whitfield ◽  
...  
Keyword(s):  
North America ◽  
New Hampshire ◽  
New World ◽  
Phylogenetic Analyses ◽  
Eastern North America ◽  
Plant Association ◽  
Distribution Map ◽  
New Host ◽  
World Species ◽  
Allegheny Mountains

Abstract Microplitis Foerster is a highly diverse and cosmopolitan genus within Microgastrinae (Hymenoptera, Ichneumonoidea, Braconidae). Microplitis ceratomiae Riley, a widely distributed North American species, exclusively attacks sphingid caterpillars. In this paper, M. ceratomiae is reported parasitizing a caterpillar of Sphinx poecila Stephens (Sphingidae) which was collected feeding on Spiraea alba Du Roi (Rosaceae), a species of white meadowsweet native to the wet soils of the Allegheny Mountains and other portions of eastern North America. Here, we report and describe this new host-parasitoid-food plant association in southern New Hampshire, and include a distribution map for the species. Biological, ecological and phylogenetic analyses, and an identification key for the nine known species of Microplitis that attack sphingids in the New World are provided.

scholarly journals Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions

2019 ◽  
Vol 116 (22) ◽  
pp. 10734-10743 ◽  
Author(s):  
Hugo K. Dooner ◽  
Qinghua Wang ◽  
Jun T. Huang ◽  
Yubin Li ◽  
Limei He ◽  
...  
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Ltr Retrotransposons ◽  
Spontaneous Mutations ◽  
Maize Pollen ◽  
Genome Wide ◽  
Autonomous Element ◽  
Low Copy Number ◽  
Female Germline

While studying spontaneous mutations at the maizebronze(bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate newbzmutations from severalBzstocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stablebzmutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneouswxmutations [Wessler S (1997)The Mutants of Maize, pp 385–386]. Similar mutations were recovered at the closely linkedshlocus. These events occurred with a frequency of 2–4 × 10−5in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, likeHopscotch,Magellan, andBs2, aBs1variant, were described previously; others, likeFotoandFocouin 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition ofHopscotch,Magellan, andBs2occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.

scholarly journals Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

2019 ◽  
Author(s):  
Eva F. Caceres ◽  
William H. Lewis ◽  
Felix Homa ◽  
Tom Martin ◽  
Andreas Schramm ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Metagenomic Data ◽  
Endosomal Sorting ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Complete Genomes ◽  
Culture Independent ◽  
Long Read

AbstractAsgard archaea is a recently proposed superphylum currently comprised of five recognised phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota and Helarchaeota. Members of this group have been identified based on culture-independent approaches with several metagenome-assembled genomes (MAGs) reconstructed to date. However, most of these genomes consist of several relatively small contigs, and, until recently, no complete Asgard archaea genome is yet available. Large scale phylogenetic analyses suggest that Asgard archaea represent the closest archaeal relatives of eukaryotes. In addition, members of this superphylum encode proteins that were originally thought to be specific to eukaryotes, including components of the trafficking machinery, cytoskeleton and endosomal sorting complexes required for transport (ESCRT). Yet, these findings have been questioned on the basis that the genome sequences that underpin them were assembled from metagenomic data, and could have been subjected to contamination and other assembly artefacts. Even though several lines of evidence indicate that the previously reported findings were not affected by these issues, having access to high-quality and preferentially fully closed Asgard archaea genomes is needed to definitively close this debate. Current long-read sequencing technologies such as Oxford Nanopore allow the generation of long reads in a high-throughput manner making them suitable for their use in metagenomics. Although the use of long reads is still limited in this field, recent analyses have shown that it is feasible to obtain complete or near-complete genomes of abundant members of mock communities and metagenomes of various level of complexity. Here, we show that long read metagenomics can be successfully applied to obtain near-complete genomes of low-abundant members of complex communities from sediment samples. We were able to reconstruct six MAGs from different Lokiarchaeota lineages that show high completeness and low fragmentation, with one of them being a near-complete genome only consisting of three contigs. Our analyses confirm that the eukaryote-like features previously associated with Lokiarchaeota are not the result of contamination or assembly artefacts, and can indeed be found in the newly reconstructed genomes.

scholarly journals The human ribosomal DNA array is composed of highly homogenized tandem clusters

2021 ◽  
Author(s):  
Yutaro Hori ◽  
Akira Shimamoto ◽  
Takehiko Kobayashi
Keyword(s):  
Ribosomal Dna ◽  
Copy Number ◽  
Large Scale ◽  
Human Cells ◽  
Nanopore Sequencing ◽  
Cellular Functions ◽  
Rdna Cluster ◽  
Repetitive Nature ◽  
Long Read ◽  
Rdna Copy

The structure of the human ribosomal DNA (rDNA) cluster has traditionally been hard to analyze owing to its highly repetitive nature. However, the recent development of long-read sequencing technology, such as Oxford Nanopore sequencing, has enabled us to study the large-scale structure of the genome. Using this technology, we found that human cells have a quite regular rDNA structure. Although each human rDNA copy has some variations in its noncoding region, contiguous copies of rDNA are similar, suggesting that homogenization through gene conversion frequently occurs between copies. Analysis of rDNA methylation by Nanopore sequencing further showed that all the noncoding regions are heavily methylated, whereas about half of the coding regions are clearly unmethylated. The ratio of unmethylated copies, which are speculated to be transcriptionally active, was lower in individuals with a higher rDNA copy number, suggesting that there is a mechanism that keeps the active copy number stable. In addition, the rDNA in progeroid syndrome patient cells with reduced DNA repair activity had more unstable copies compared with control normal cells, although the rate was much lower than previously reported using a fiber-FISH method. Collectively, our results clarify the view of rDNA stability and transcription regulation in human cells, indicating the presence of mechanisms for both homogenizations to ensure sequence quality and maintenance of active copies for cellular functions.

scholarly journals Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

Science ◽  
2019 ◽  
Vol 366 (6463) ◽  
pp. eaax2083 ◽  
Author(s):  
PingHsun Hsieh ◽  
Mitchell R. Vollger ◽  
Vy Dang ◽  
David Porubsky ◽  
Carl Baker ◽  
...  
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Sequence Data ◽  
Local Population ◽  
Copy Number Variants ◽  
Human Populations ◽  
Single Nucleotide Variants ◽  
Human Genes ◽  
Long Read ◽  
Archaic Introgression

Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.

Studies in Neotropical Araliaceae. II. Resurrection of the Neotropical Genus Crepinella for a Clade of New World Species Previously Included in Schefflera (Araliaceae)

2019 ◽  
Vol 27 (4) ◽  
pp. 253-261 ◽  
Author(s):  
Porter P. Lowry II ◽  
Gregory M. Plunkett ◽  
David A. Neill
Keyword(s):  
New World ◽  
Guiana Shield ◽  
New Combinations ◽  
World Species ◽  
Southwest Pacific ◽  
Separate Genus ◽  
Montane Vegetation ◽  
Infraspecific Taxa

The pantropical genus Schefflera J. R. Forst. & G. Forst. (Araliaceae) was recently found to be polyphyletic, making it necessary to restrict the generic name to a small clade in the southwest Pacific and to transfer the members of the four remaining clades to other genera. Recent studies of the Neotropical clade have shown that it comprises five morphologically and geographically coherent subclades, each of which is being recognized as a separate genus. In the present synopsis, Crepinella Marchal is resurrected to include the 33 currently recognized species and four infraspecific taxa belonging to one of these subclades, necessitating 36 new combinations (32 species, two subspecies, and two varieties); two names are also lectotypified. Members of Crepinella can be recognized by their leaves with coriaceous leaflets and small stipular ligules, compoundumbellate inflorescences, and 2- to 5-carpellate ovaries, coupled with a distribution that is largely restricted to montane vegetation on the sandstone tepuis of the Guiana Shield, with just three species occurring on sandstone substrates elsewhere in Brazil, Colombia, Ecuador, and Peru.

scholarly journals ERV-L Elements: a Family of Endogenous Retrovirus-Like Elements Active throughout the Evolution of Mammals

1999 ◽  
Vol 73 (4) ◽  
pp. 3301-3308 ◽  
Author(s):  
Laurence Bénit ◽  
Jean-Baptiste Lallemand ◽  
Jean-François Casella ◽  
Hervé Philippe ◽  
Thierry Heidmann
Keyword(s):  
Copy Number ◽  
Southern Blot Analysis ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Endogenous Retrovirus ◽  
Evolutionary Scheme ◽  
Low Copy Number ◽  
Genomic Dnas ◽  
Evolution Of Mammals ◽  
High Level

ABSTRACT We have previously identified in the human genome a family of 200 endogenous retrovirus-like elements, the HERV-L elements, disclosing similarities with the foamy retroviruses and which might be the evolutionary intermediate between classical intracellular retrotransposons and infectious retroviruses. Southern blot analysis of a large series of mammalian genomic DNAs shows that HERV-L-related elements—so-called ERV-L—are present among all placental mammals, suggesting that ERV-L elements were already present at least 70 million years ago. Most species exhibit a low copy number of ERV-L elements (from 10 to 30), while simians (not prosimians) and mice (not rats) have been subjected to bursts resulting in increases in the number of copies up to 200. The burst of copy number in primates can be dated to shortly after the prosimian and simian branchpoint, 45 to 65 million years ago, whereas murine species have been subjected to two much more recent bursts (less than 10 million years ago), occurring after theMus/Rattus split. We have amplified and sequenced 360-bp ERV-L internal fragments of the highly conserved pol gene from a series of 22 mammalian species. These sequences exhibit high percentages of identity (57 to 99%) with the murine fully coding MuERV-L element. Phylogenetic analyses allowed the establishment of a plausible evolutionary scheme for ERV-L elements, which accounts for the high level of sequence conservation and the widespread dispersion among mammals.

A new combination in Alkekengi (Solanaceae) for the Flora of China

Phytotaxa ◽  
2014 ◽  
Vol 178 (1) ◽  
pp. 59 ◽  
Author(s):  
Ruijiang Wang
Keyword(s):  
Vascular Plants ◽  
New World ◽  
Phylogenetic Analyses ◽  
New Combination ◽  
Monotypic Genus ◽  
World Species ◽  
Nomenclature Committee ◽  
Flora Of China ◽  
The Family ◽  
Eurasian Species

The genus Physalis Linnaeus (1753: 182) is a medium-sized genus in the family Solanaceae Jussieu (1789: 124). It includes about 75 New World species and one Eurasian species, P. alkekengi Linnaeus (1753: 183), the generic lectotype (Britton & Brown 1913). Recently, several phylogenetic analyses focusing on Physalis and related taxa strongly supported the monophyly of the morphologically typical New World species, characterized by unlobed and yellow flowers. Physalis alkekengi represents a divergent clade characterized by somewhat lobed, white corollas and brilliant red-orange fruiting calyces (Whitson & Manos 2005; Olmstead et al. 2008). In order to emphasize the monophyly and morphological homogeneity of the New World species and decrease nomenclatural disruption, the genus Physalis was proposed for conservation with a conserved type, P. pubescens Linneaus, to represent the New World species (Whitson 2011). The Eurasian P. alkekengi was suggested to be placed in a monotypic genus Alkekengi Miller (1754: AL) typified with A. officinarum Moench (1802: 177). This proposal was subsequently recommended for acceptance by the Nomenclature Committee for Vascular Plants (Applequist 2012).

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