Updated single cell reference atlas for the starlet anemone Nematostella vectensis

BACKGROUND

The recent combination of genomics and single cell transcriptomics has allowed to assess a variety of non-conventional model organisms in much more depth. Single cell transcriptomes can uncover hidden cellular complexity and cell lineage relationships within organisms. The recent developmental cell atlases of the sea anemone Nematostella vectensis, a representative of the basally branching Cnidaria, has provided new insights into the development of all cell types (Steger et al Cell Rep 40(12):111370, 2022; Sebé-Pedrós et al. Cell 173(6):1520-1534.e20). However, the mapping of the single cell reads still suffers from relatively poor gene annotations and a draft genome consisting of many scaffolds.

RESULTS

Here we present a new wildtype resource of the developmental single cell atlas, by re-mapping of sequence data first published in Steger et al. (2022) and Cole et al. (Nat Commun 14(1):1747, 2023), to the new chromosome-level genome assembly and corresponding gene models in Zimmermann et al. (Nat Commun 14, 8270 (2023). https://doi.org/10.1038/s41467-023-44080-7 ). We expand the pre-existing dataset through the incorporation of additional sequence data derived from the capture and sequencing of cell suspensions from four additional samples: 24 h gastrula, 2d planula, an inter-parietal region of the bodywall from a young unsexed animal, and another adult mesentery from a mature male animal.

CONCLUSION

Our analyses of the full cell-state inventory provide transcriptomic signatures for 127 distinct cell states, of which 47 correspond to neuroglandular subtypes. We also identify two distinct putatively immune-related transcriptomic profiles that segregate between the inner and outer cell layers. Furthermore, the new gene annotation Nv2 has markedly improved the mapping on the single cell transcriptome data and will therefore be of great value for the community and anyone using the dataset.

[Translated article] Less superior adjacent syndrome and lower reoperation rate. Medium- and long-term results of cervical arthroplasty versus anterior cervical arthrodesis: Systematic review and meta-analysis of randomized clinical trials

OBJECTIVE

To compare medium- and long-term postoperative surgical results, especially the adjacent syndrome rate, adverse event rate, and reoperation rate, of patients operated on with cervical arthroplasty or anterior cervical arthrodesis in published randomized clinical trials (RCTs), at one cervical level.

METHODS

Systematic review and meta-analysis. Thirteen RCTs were selected. The clinical, radiological and surgical results were analyzed, taking the adjacent syndrome rate and the reoperation rate as the primary objective of the study.

RESULTS

Two thousand nine hundred and sixty three patients were analyzed. The cervical arthroplasty group showed a lower rate of superior adjacent syndrome (P<0.001), lower reoperation rate (P<0.001), less radicular pain (P=0.002), and a better score of neck disability index (P=0.02) and SF-36 physical component (P=0.01). No significant differences were found in the lower adjacent syndrome rate, adverse event rate, neck pain scale, or SF-36 mental component. A range of motion of 7.91° was also found at final follow-up, and a heterotopic ossification rate of 9.67% in patients with cervical arthroplasty.

CONCLUSION

In the medium and long-term follow-up, cervical arthroplasty showed a lower rate of superior adjacent syndrome and a lower rate of reoperation. No statistically significant differences were found in the rate of inferior adjacent syndrome or in the rate of adverse events.

Less superior adjacent syndrome and lower reoperation rate. Medium- and long-term results of cervical arthroplasty versus anterior cervical arthrodesis: Systematic review and meta-analysis of randomized clinical trials

OBJECTIVE

To compare medium- and long-term postoperative surgical results, especially the adjacent syndrome rate, adverse event rate, and reoperation rate, of patients operated on with cervical arthroplasty or anterior cervical arthrodesis in published randomized clinical trials (RCTs), at one cervical level.

METHODS

Systematic review and meta-analysis. Thirteen RCTs were selected. The clinical, radiological and surgical results were analyzed, taking the adjacent syndrome rate and the reoperation rate as the primary objective of the study.

RESULTS

Two thousand nine hundred and sixty three patients were analyzed. The cervical arthroplasty group showed a lower rate of superior adjacent syndrome (P<0.001), lower reoperation rate (P<0.001), less radicular pain (P=0.002), and a better score of neck disability index (P=0.02) and SF-36 physical component (P=0.01). No significant differences were found in the lower adjacent syndrome rate, adverse event rate, neck pain scale, or SF-36 mental component. A range of motion of 7.91 degrees was also found at final follow-up, and a heterotopic ossification rate of 9.67% in patients with cervical arthroplasty.

CONCLUSION

In the medium and long-term follow-up, cervical arthroplasty showed a lower rate of superior adjacent syndrome and a lower rate of reoperation. No statistically significant differences were found in the rate of inferior adjacent syndrome or in the rate of adverse events.

Topological structures and syntenic conservation in sea anemone genomes

There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.

Arthroscopic rotator cuff repair using a single or double row technique: A meta-analysis of randomized clinical trial

PURPOSE

To compare the double row technique versus the single row technique for arthroscopic rotator cuff repair, in order to assess whether there are clinical differences.

METHODS

Systematic review of randomized clinical trials comparing the clinical results of the double-row technique versus the single-row technique in arthroscopic rotator cuff repair. Demographic, clinical, and surgical variables were analyzed, including functional scores, tendon healing rate, and re-tear rate.

RESULTS

Thirteen randomized clinical trials were selected. 437 patients in the single row group (50.7%) and 424 patients in the double row group (49.3%) were analyzed. No significant differences were found between the two groups in terms of age (P=.84), sex (P=.23) and loss to follow-up (P=.52). Significant differences were found for the better results of the double row technique at the UCLA level (P=.01). No significant differences were found on the Constant-Murley scale (P=.87) or on the ASES scale (P=.56). Similarly, there was a higher healing rate (P=.006) and less risk of rotator cuff re-tears with the double row technique (P=.006).

CONCLUSIONS

In rotator cuff repair, the double row technique was found to be superior to the single row technique in terms of better UCLA score, better tendon healing rate, and lower re-tear rate. No clinically significant differences were found on the Constant-Murley scale or on the ASES scale.

Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. 'INIA 601'

Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace 'Kculli', but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar 'INIA 601' with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America.

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.

Gene Co-expression Network Analysis

Gene co-expression analysis is a data analysis technique that helps identify groups of genes with similar expression patterns across several different conditions. By means of these techniques, different groups have been able to assign putative metabolic pathways and functions to understudied genes and to identify novel metabolic regulation networks for different metabolites. Some groups have even used network comparative studies to understand the evolution of these networks from green algae to land plants. In this chapter, we will go over the basic definitions required to understand network topology and gene module identification. Additionally, we offer the reader a walk-through a standard analysis pipeline as implemented in the package WGCNA that takes as input raw fastq files and obtains co-expressed gene clusters and representative gene expression patterns from each module for downstream applications.

Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing

Identifying the geographic origins of crops is important for the conservation and utilization of novel genetic variation. Even so, the origins of many food crops remain elusive. The tree nut crop macadamia has a remarkable domestication history, from subtropical rain forests in Australia through Hawaii to global cultivation all within the last century. The industry is based primarily on Macadamia integrifolia and M. integrifolia-M. tetraphylla hybrid cultivars with Hawaiian cultivars the main contributors to world production. Sequence data from the chloroplast genome assembled using a genome skimming strategy was used to determine population structure among remnant populations of the main progenitor species, M. integrifolia. Phylogenetic analysis of a 506 bp chloroplast SNP alignment from 64 wild and cultivated accessions identified phylogeographic structure and deep divergences between clades providing evidence for historical barriers to seed dispersal. High levels of variation were detected among wild accessions. Most Hawaiian cultivars, however, shared a single chlorotype that was also present at two wild sites at Mooloo and Mt Bauple from the northernmost distribution of the species in south-east Queensland. Our results provide evidence for a maternal genetic bottleneck during early macadamia domestication, and pinpoint the likely source of seed used to develop the Hawaiian cultivars. The extensive variability and structuring of M. integrifolia chloroplast genomic variation detected in this study suggests much unexploited genetic diversity is available for improvement of this recently domesticated crop.

Molecular and genetic characterization of the Ryadg locus on chromosome XI from Andigena potatoes conferring extreme resistance to potato virus Y

KEY MESSAGE

We have elucidated the Andigena origin of the potato Ryadg gene on chromosome XI of CIP breeding lines and developed two marker assays to facilitate its introgression in potato by marker-assisted selection. Potato virus Y (PVY) is causing yield and quality losses forcing farmers to renew periodically their seeds from clean stocks. Two loci for extreme resistance to PVY, one on chromosome XI and the other on XII, have been identified and used in breeding. The latter corresponds to a well-known source of resistance (Solanum stoloniferum), whereas the one on chromosome XI was reported from S. stoloniferum and S. tuberosum group Andigena as well. To elucidate its taxonomic origin in our breeding lines, we analyzed the nucleotide sequences of tightly linked markers (M45, M6) and screened 251 landraces of S. tuberosum group Andigena for the presence of this gene. Our results indicate that the PVY resistance allele on chromosome XI in our breeding lines originated from S. tuberosum group Andigena. We have developed two marker assays to accelerate the introgression of Ryadg gene into breeding lines by marker-assisted selection (MAS). First, we have multiplexed RYSC3, M6 and M45 DNA markers flanking the Ryadg gene and validated it on potato varieties with known presence/absence of the Ryadg gene and a progeny of 6,521 individuals. Secondly, we developed an allele-dosage assay particularly useful to identify multiplex Ryadg progenitors. The assay based on high-resolution melting analysis at the M6 marker confirmed Ryadg plex level as nulliplex, simplex and duplex progenitors and few triplex progenies. These marker assays have been validated and can be used to facilitate MAS in potato breeding.

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.

The pangenome of hexaploid bread wheat

There is an increasing understanding that variation in gene presence-absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene presence-absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 ± 102 genes, a core genome of 81 070 ± 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal single nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at http://appliedbioinformatics.com.au/cgi-bin/gb2/gbrowse/WheatPan/, and data are available to download from http://wheatgenome.info/wheat_genome_databases.php.

Ex-post analysis of landraces sympatric to a commercial variety in the center of origin of the potato failed to detect gene flow

The possible introduction of genetically modified potato in the Andean region raises concerns about the unintentional introduction of transgenes into the native potato germplasm because it is perceived to convey negative impacts on biodiversity. We investigated this question by an ex-post analysis of existing landraces resulting from natural hybridization between an unknown landrace and the fertile commercial variety ‘Yungay’. This variety can be regarded as exotic because it was bred in part from the southern Chilean germplasm of Solanum tuberosum Group Chilotanum. We sampled the landrace germplasm of 1,771 leaf samples comprising more than 400 different landraces from three regions where ‘Yungay’ and landraces have coexisted for 15–25 years in the Peruvian Andes. Simple sequence repeat (SSR) markers were used to identify putative hybrids based on allele sharing with those of ‘Yungay’. The exclusion procedure was iterative, starting with the SSR markers with highest discriminating capacity based on allele frequency of the variety ‘Yungay’ in our large database of 688 landraces by 24 SSR makers. With only 12 of the 24 SSR markers assayed, all of the samples could be rejected as possible hybrids with ‘Yungay’ as a parent. This result demonstrates that the unintentional introduction of a transgene, not under farmers’ selection, from a widely grown transgenic variety over a long period of time is unlikely to happen at a detectable scale. Our finding reinforces the prominent role of farmers in the selection and maintenance of landraces which, unlike hybrids, have specific characteristics that farmers appreciate.