Nanopore sequencing with T2T-CHM13 for accurate detection and preventing the transmission of structural rearrangements in highly repetitive heterochromatin regions in human embryos

BACKGROUND

Structural rearrangements in highly repetitive heterochromatin regions can result in miscarriage or foetal malformations; however, detecting and preventing the transmission of these rearrangements has been challenging. Recently, the completion of sequencing of the complete human genome (T2T-CHM13) has made it possible to accurately characterise structural rearrangements in these regions. We developed a method based on T2T-CHM13 and nanopore sequencing to detect and block structural rearrangements in highly repetitive heterochromatin sequences.

METHODS

T2T-CHM13-based "Mapping Allele with Resolved Carrier Status" was performed for couples who carry structural rearrangements in heterochromatin regions. Using nanopore sequencing and the T2T-CHM13 reference genome, the precise breakpoints of inversions and translocations close to the centromere were detected and haplotypes were constructed using flanking single-nucleotide polymorphisms (SNPs). Haplotype linkage analysis was then performed by comparing consistent parental SNPs with embryonic SNPs to determine whether the embryos carried hereditary inversions or balanced translocations. Based on copy number variation and haplotype linkage analysis, we transplanted normal embryos, which were further verified by an amniotic fluid test.

RESULTS

To validate this approach, we used nanopore sequencing of families with inversions and reciprocal translocations close to the centromere. Using the T2T-CHM13 reference genome, we accurately detected inversions and translocations in centromeres, constructed haplotypes and prevented the transmission of structural rearrangements in the offspring.

CONCLUSIONS

This study represents the first successful application of T2T-CHM13 in human reproduction and provides a feasible protocol for detecting and preventing the transmission of structural rearrangements of heterochromatin in embryos.

A Rare Case of Concurrent 2q34q36 Duplication and 2q37 Deletion in a Neonate with Syndromic Features

Large-scale genomic structural variations can have significant clinical implications, depending on the specific altered genomic region. Briefly, 2q37 microdeletion syndrome is a prevalent subtelomeric deletion disorder characterized by variable-sized deletions. Affected patients exhibit a wide range of clinical manifestations, including short stature, facial dysmorphism, and features of autism spectrum disorder, among others. Conversely, isolated duplications of proximal chromosome 2q are rare and lack a distinct phenotype. In this report, we provide an extensive molecular analysis of a 15-day-old newborn referred for syndromic features. Our analysis reveals an 8.5 Mb microdeletion at 2q37.1, which extends to the telomere, in conjunction with an 8.6 Mb interstitial microduplication at 2q34q36.1. Our findings underscore the prominence of 2q37 terminal deletions as commonly reported genomic anomalies. We compare our patient's phenotype with previously reported cases in the literature to contribute to a more refined classification of 2q37 microdeletion syndrome and assess the potential impact of 2q34q36.1 microduplication. We also investigate multiple hypotheses to clarify the genetic mechanisms responsible for the observed genomic rearrangement.

ESHRE PGT Consortium data collection XXI: PGT analyses in 2018

STUDY QUESTION

What are the trends and developments in preimplantation genetic testing (PGT) in 2018 as compared to previous years?

SUMMARY ANSWER

The main trends observed in this 21st dataset on PGT are that the implementation of trophectoderm biopsy with comprehensive whole-genome testing is most often applied for PGT-A and concurrent PGT-M/SR/A, while for PGT-M and PGT-SR, single-cell testing with PCR and FISH still prevail.

WHAT IS KNOWN ALREADY

Since it was established in 1997, the ESHRE PGT Consortium has been collecting and analysing data from mainly European PGT centres. To date, 20 datasets and an overview of the first 10 years of data collections have been published.

STUDY DESIGN SIZE DURATION

The data for PGT analyses performed between 1 January 2018 and 31 December 2018 with a 2-year follow-up after analysis were provided by participating centres on a voluntary basis. Data were collected using an online platform, which is based on genetic analysis and has been in use since 2016.

PARTICIPANTS/MATERIALS SETTING METHODS

Data on biopsy method, diagnostic technology, and clinical outcome were submitted by 44 centres. Records with analyses for more than one PGT for monogenic disorders (PGT-M) and/or PGT for chromosomal structural rearrangements (PGT-SR), or with inconsistent data regarding the PGT modality, were excluded. All transfers performed within 2 years after the analysis were included, enabling the calculation of cumulative pregnancy rates. Data analysis, calculations, and preparation of figures and tables were carried out by expert co-authors.

MAIN RESULTS AND THE ROLE OF CHANCE

The current data collection from 2018 covers a total of 1388 analyses for PGT-M, 462 analyses for PGT-SR, 3003 analyses for PGT for aneuploidies (PGT-A), and 338 analyses for concurrent PGT-M/SR with PGT-A.The application of blastocyst biopsy is gradually rising for PGT-M (from 19% in 2016-2017 to 33% in 2018), is status quo for PGT-SR (from 30% in 2016-2017 to 33% in 2018) and has become the most used biopsy stage for PGT-A (from 87% in 2016-2017 to 98% in 2018) and for concurrent PGT-M/SR with PGT-A (96%). The use of comprehensive, whole-genome amplification (WGA)-based diagnostic technology showed a small decrease for PGT-M (from 15% in 2016-2017 to 12% in 2018) and for PGT-SR (from 50% in 2016-2017 to 44% in 2018). Comprehensive testing was, however, the main technology for PGT-A (from 93% in 2016-2017 to 98% in 2018). WGA-based testing was also widely used for concurrent PGT-M/SR with PGT-A, as a standalone technique (74%) or in combination with PCR or FISH (24%). Trophectoderm biopsy and comprehensive testing strategies are linked with higher diagnostic efficiencies and improved clinical outcomes per embryo transfer.

LIMITATIONS REASONS FOR CAUTION

The findings apply to the data submitted by 44 participating centres and do not represent worldwide trends in PGT. Details on the health of babies born were not provided in this manuscript.

WIDER IMPLICATIONS OF THE FINDINGS

The Consortium datasets provide a valuable resource for following trends in PGT practice.

STUDY FUNDING/COMPETING INTERESTS

The study has no external funding, and all costs are covered by ESHRE. There are no competing interests declared.

TRIAL REGISTRATION NUMBER

N/A.

On the Origin of Neo-Sex Chromosomes in the Neotropical Dragonflies Rhionaeschna bonariensis and R. planaltica (Aeshnidae, Odonata)

Odonata have holokinetic chromosomes. About 95% of species have an XX/X0 sex chromosome system, with heterogametic males. There are species with neo-XX/neo-XY sex chromosomes resulting from an X chromosome/autosome fusion. The genus Rhionaeschna includes 42 species found in the Americas. We analyzed the distribution of the nucleolar organizer region (NOR) using FISH with rDNA probes in Rhionaeschna bonariensis (n = 12 + neo-XY), R. planaltica (n = 7 + neo-XY), and Aeshna cyanea (n = 13 + X0). In R. bonariensis and A. cyanea, the NOR is located on a large pair of autosomes, which have a secondary constriction in the latter species. In R. planaltica, the NOR is located on the ancestral part of the neo-X chromosome. Meiotic analysis and FISH results in R. planaltica led to the conclusion that the neo-XY system arose by insertion of the ancestral X chromosome into an autosome. Genomic in situ hybridization, performed for the first time in Odonata, highlighted the entire neo-Y chromosome in meiosis of R. bonariensis, suggesting that it consists mainly of repetitive DNA. This feature and the terminal chiasma localization suggest an ancient origin of the neo-XY system. Our study provides new information on the origin and evolution of neo-sex chromosomes in Odonata, including new types of chromosomal rearrangements, NOR transposition, and heterochromatin accumulation.

Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation

In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.

Inversion invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow

Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large inversions that arise early in divergence. Why this occurs has yet to be resolved. To address this gap, we built forward-time simulations in which inversions have flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for a highly polygenic trait. In our simulations, inversions typically arose early in divergence, captured standing genetic variation upon mutation, and then accumulated many small-effect loci over time. Under special conditions, inversions could also arise late in adaptation and capture locally adapted alleles. Polygenic inversions behaved similarly to a single supergene of large effect and were detectable by genome scans. Our results show that characteristics of adaptive inversions found in empirical studies (e.g. multiple large, old inversions that are F_ST outliers, sometimes overlapping with other inversions) are consistent with a highly polygenic architecture, and inversions do not need to contain any large-effect genes to play an important role in local adaptation. By combining a population and quantitative genetic framework, our results give a deeper understanding of the specific conditions needed for inversions to be involved in adaptation when the genetic architecture is polygenic. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.

ESHRE PGT Consortium data collection XIX-XX: PGT analyses from 2016 to 2017†

STUDY QUESTION

What are the trends and developments in pre-implantation genetic testing (PGT) in 2016–2017 as compared to previous years?

SUMMARY ANSWER

The main trends observed in this 19th and 20th data set on PGT are that trophectoderm biopsy has become the main biopsy stage for PGT for aneuploidies (PGT-A) and that the implementation of comprehensive testing technologies is the most advanced with PGT-A.

WHAT IS KNOWN ALREADY

Since it was established in 1997, the ESHRE PGT Consortium has been collecting and analysing data from mainly European PGT centres. To date, 18 data sets and an overview of the first 10 years of data collections have been published.

STUDY DESIGN, SIZE, DURATION

The data for PGT analyses performed between 1 January 2016 and 31 December 2017 with a 2-year follow-up after analysis were provided by participating centres on a voluntary basis. Data were collected using a new online platform, which is based on genetic analysis as opposed to the former cycle-based format.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Data on biopsy method, diagnostic technology and clinical outcome were submitted by 61 centres. Records with analyses for more than one PGT for monogenic/single gene defects (PGT-M) and/or PGT for chromosomal structural rearrangements (PGT-SR) indication or with inconsistent data regarding the PGT modality were excluded. All transfers performed within 2 years after the analysis were included enabling the calculation of cumulative pregnancy rates. Data analysis, calculations, figures and tables were made by expert co-authors.

MAIN RESULTS AND THE ROLE OF CHANCE

The current data collection from 2016 to 2017 covers a total of 3098 analyses for PGT-M, 1018 analyses for PGT-SR, 4033 analyses for PGT-A and 654 analyses for concurrent PGT-M/SR with PGT-A.

The application of blastocyst biopsy is gradually rising for PGT-M (from 8–12% in 2013–2015 to 19% in 2016–2017), is status quo for PGT-R (from 22–36% in 2013–2015 to 30% in 2016–2017) and has become the preferential biopsy stage for PGT-A (from 23–36% in 2013–2015 to 87% in 2016–2017). For concurrent PGT-M/SR with PGT-A, biopsy was primarily performed at the blastocyst stage (93%). The use of comprehensive diagnostic technology showed a similar trend with a small increased use for PGT-M (from 9–12% in 2013–2015 to 15% in 2016–2017) and a status quo for PGT-SR (from 36–58% in 2013–2015 to 50% in 2016–2017). Comprehensive testing was the main technology for PGT-A (from 66–75% in 2013–2015 to 93% in 2016–2017) and for concurrent PGT-M/SR with PGT-A (93%).

LIMITATIONS, REASONS FOR CAUTION

The findings apply to the data submitted by 61 participating centres and do not represent worldwide trends in PGT. Details on the health of babies born were not provided in this manuscript.

WIDER IMPLICATIONS OF THE FINDINGS

Being the largest data collection on PGT in Europe/worldwide, the data sets provide a valuable resource for following trends in PGT practice.

STUDY FUNDING/COMPETING INTEREST(S)

The study has no external funding and all costs are covered by ESHRE. There are no competing interests declared.

TRIAL REGISTRATION NUMBER

N/A.

Comprehensive preimplantation genetic testing by massively parallel sequencing

STUDY QUESTION

Can whole genome sequencing (WGS) offer a relatively cost-effective approach for embryonic genome-wide haplotyping and preimplantation genetic testing (PGT) for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR)?

SUMMARY ANSWER

Reliable genome-wide haplotyping, PGT-M, PGT-A and PGT-SR could be performed by WGS with 10× depth of parental and 4× depth of embryonic sequencing data.

WHAT IS KNOWN ALREADY

Reduced representation genome sequencing with a genome-wide next-generation sequencing haplarithmisis-based solution has been verified as a generic approach for automated haplotyping and comprehensive PGT. Several low-depth massively parallel sequencing (MPS)-based methods for haplotyping and comprehensive PGT have been developed. However, an additional family member, such as a sibling, or a proband, is required for PGT-M haplotyping using low-depth MPS methods.

STUDY DESIGN, SIZE, DURATION

In this study, 10 families that had undergone traditional IVF-PGT and 53 embryos, including 13 embryos from two PGT-SR families and 40 embryos from eight PGT-M families, were included to evaluate a WGS-based method. There were 24 blastomeres and 29 blastocysts in total. All embryos were used for PGT-A. Karyomapping validated the WGS results. Clinical outcomes of the 10 families were evaluated.

PARTICIPANTS/MATERIALS, SETTING, METHODS

A blastomere or a few trophectoderm cells from the blastocyst were biopsied, and multiple displacement amplification (MDA) was performed. MDA DNA and bulk DNA of family members were used for library construction. Libraries were sequenced, and data analysis, including haplotype inheritance deduction for PGT-M and PGT-SR and read-count analysis for PGT-A, was performed using an in-house pipeline. Haplotyping with a proband and parent-only haplotyping without additional family members were performed to assess the WGS methodology. Concordance analysis between the WGS results and traditional PGT methods was performed.

MAIN RESULTS AND THE ROLE OF CHANCE

For the 40 PGT-M and 53 PGT-A embryos, 100% concordance between the WGS and single-nucleotide polymorphism (SNP)-array results was observed, regardless of whether additional family members or a proband was included for PGT-M haplotyping. For the 13 embryos from the two PGT-SR families, the embryonic balanced translocation was detected and 100% concordance between WGS and MicroSeq with PCR-seq was demonstrated.

LIMITATIONS, REASONS FOR CAUTION

The number of samples in this study was limited. In some cases, the reference embryo for PGT-M or PGT-SR parent-only haplotyping was not available owing to failed direct genotyping.

WIDER IMPLICATIONS OF THE FINDINGS

WGS-based PGT-A, PGT-M and PGT-SR offered a comprehensive PGT approach for haplotyping without the requirement for additional family members. It provided an improved complementary method to PGT methodologies, such as low-depth MPS- and SNP array-based methods.

STUDY FUNDING/COMPETING INTEREST(S)

This research was supported by the research grant from the National Key R&D Program of China (2018YFC0910201 and 2018YFC1004900), the Guangdong province science and technology project of China (2019B020226001), the Shenzhen Birth Defect Screening Project Lab (JZF No. [2016] 750) and the Shenzhen Municipal Government of China (JCYJ20170412152854656). This work was also supported by the National Natural Science Foundation of China (81771638, 81901495 and 81971344), the National Key R&D Program of China (2018YFC1004901 and 2016YFC0905103), the Shanghai Sailing Program (18YF1424800), the Shanghai Municipal Commission of Science and Technology Program (15411964000) and the Shanghai 'Rising Stars of Medical Talent' Youth Development Program Clinical Laboratory Practitioners Program (201972). The authors declare no competing interests.

TRIAL REGISTRATION NUMBER

N/A.

Horse Clinical Cytogenetics: Recurrent Themes and Novel Findings

Clinical cytogenetic studies in horses have been ongoing for over half a century and clearly demonstrate that chromosomal disorders are among the most common non-infectious causes of decreased fertility, infertility, and congenital defects. Large-scale cytogenetic surveys show that almost 30% of horses with reproductive or developmental problems have chromosome aberrations, whereas abnormal karyotypes are found in only 2-5% of the general population. Among the many chromosome abnormalities reported in the horse, most are unique or rare. However, all surveys agree that there are two recurrent conditions: X-monosomy and SRY-negative XY male-to-female sex reversal, making up approximately 35% and 11% of all chromosome abnormalities, respectively. The two are signature conditions for the horse and rare or absent in other domestic species. The progress in equine genomics and the development of molecular tools, have qualitatively improved clinical cytogenetics today, allowing for refined characterization of aberrations and understanding the underlying molecular mechanisms. While cutting-edge genomics tools promise further improvements in chromosome analysis, they will not entirely replace traditional cytogenetics, which still is the most straightforward, cost-effective, and fastest approach for the initial evaluation of potential breeding animals and horses with reproductive or developmental disorders.

Next generation sequencing of breast implant-associated anaplastic large cell lymphomas reveals a novel STAT3-JAK2 fusion among other activating genetic alterations within the JAK-STAT pathway

Breast implant associated anaplastic large cell lymphoma (BIA-ALCL) is a distinct type of ALCL, and a new provisional entity by the 2016 revision of the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues. In contrast to systemic and primary cutaneous ALCLs, BIA-ALCLs have been genetically characterized by the absence of fusions and frequent activation of the JAK-STAT3 pathway through mutations in JAK1 and STAT3. In this study, we report the results of the genetic profiling of 9 BIA-ALCL cases supporting the role of the JAK-STAT pathway activation in this entity, including the identification of an activating STAT3-JAK2 fusion similar to those recently reported in T-cell lymphoproliferative disorders of the gastrointestinal tract. To our knowledge, this is the first fusion reported in BIA-ALCL, providing further insight into the overall genetic landscape of this rare entity as well as uncovering potential options for targeted therapy in cases with advanced disease.

ESHRE PGT Consortium data collection XVI-XVIII: cycles from 2013 to 2015

STUDY QUESTION

What are the trends and developments in preimplantation genetic testing (PGT) in 2013–2015 as compared to previous years?

SUMMARY ANSWER

The main trends observed in the retrospective data collections 2013–2015, representing valuable data on PGT activity in (mainly) Europe, are the increased application of trophectoderm biopsy at the cost of cleavage stage biopsy and the continuing expansion of comprehensive testing technology in PGT for chromosomal structural rearrangements and for aneuploidies (PGT-SR and PGT-A).

WHAT IS KNOWN ALREADY

Since it was established in 1997, the ESHRE PGT Consortium has been collecting data from international PGT centres. To date, 15 data sets and an overview of the first 10 years of data collections have been published.

STUDY DESIGN, SIZE, DURATION

Collection of (mainly) European data by the PGT Consortium for ESHRE. The data for PGT cycles performed between 1 January 2013 and 31 December 2015 were provided by participating centres on a voluntary basis. For the collection of cycle, pregnancy and baby data, separate, pre-designed MS Excel tables were used.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Data were submitted by 59, 60 and 59 centres respectively for 2013, 2014 and 2015 (full PGT Consortium members). Records with incomplete or inconsistent data were excluded from the calculations. Corrections, calculations, figures and tables were made by expert co-authors.

MAIN RESULTS AND THE ROLE OF CHANCE

For data collection XVI/XVII/XVIII, 59/60/59 centres reported data on 8164/9769/11 120 cycles with oocyte retrieval: 5020/6278/7155 cycles for PGT-A, 2026/2243/2661 cycles for PGT for monogenic/single gene defects, 1039/1189/1231 cycles for PGT-SR and 79/59/73 cycles for sexing for X-linked diseases. From 2013 until 2015, the uptake of biopsy at the blastocyst stage was mainly observed in cycles for PGT-A (from 23% to 36%) and PGT-SR (from 22% to 36%), alongside the increased application of comprehensive testing technology (from 66% to 75% in PGT-A and from 36% to 58% in PGT-SR).

LIMITATIONS, REASONS FOR CAUTION

The findings apply to the 59/60/59 participating centres and may not represent worldwide trends in PGT. Data were collected retrospectively and no details of the follow-up on PGT pregnancies and babies born were provided.

WIDER IMPLICATIONS OF THE FINDINGS

Being the largest data collection on PGT worldwide, detailed information about ongoing developments in the field is provided.

STUDY FUNDING/COMPETING INTEREST(S)

The study has no external funding and all costs are covered by ESHRE. There are no competing interests declared.

TRIAL REGISTRATION NUMBER

N/A.

The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These 'Choosiness-associated' CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110, that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice-the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Bridging protein structure, dynamics, and function using hydrogen/deuterium-exchange mass spectrometry

Much of our understanding of protein structure and mechanistic function has been derived from static high-resolution structures. As structural biology has continued to evolve it has become clear that high-resolution structures alone are unable to fully capture the mechanistic basis for protein structure and function in solution. Recently Hydrogen/Deuterium-exchange Mass Spectrometry (HDX-MS) has developed into a powerful and versatile tool for structural biologists that provides novel insights into protein structure and function. HDX-MS enables direct monitoring of a protein's structural fluctuations and conformational changes under native conditions in solution even as it is carrying out its functions. In this review, we focus on the use of HDX-MS to monitor these dynamic changes in proteins. We examine how HDX-MS has been applied to study protein structure and function in systems ranging from large, complex assemblies to intrinsically disordered proteins, and we discuss its use in probing conformational changes during protein folding and catalytic function. STATEMENT FOR A BROAD AUDIENCE: The biophysical and structural characterization of proteins provides novel insight into their functionalities. Protein motions, ranging from small scale local fluctuations to larger concerted structural rearrangements, often determine protein function. Hydrogen/Deuterium-exchange Mass Spectrometry (HDX-MS) has proven a powerful biophysical tool capable of probing changes in protein structure and dynamic protein motions that are often invisible to most other techniques.

Genomic Organization of the Repetitive Sequences in Centropomus undecimalis (Perciformes, Centropomidae): Implications for Hybridization and Aquaculture Programs

The family Centropomidae includes a number of fish species of high commercial value. One of these species, Centropomus undecimalis, is a target of artisanal, industrial, and sports fisheries and has also considerable potential for captive breeding, which has led to its inclusion in several aquaculture programs. While the biology and ecology of C. undecimalis are relatively well documented, few karyological data are available on this species, and they are still scarce for other centropomids. The few chromosomal data available on this family indicate a conserved karyotype 2n = 48, but it is unclear whether the chromosome microstructure is also conserved. In this study, new cytogenetic data are presented on C. undecimalis from the Amazon coastal zone, including C-banding, Ag-NOR, in situ hybridization with repetitive DNA probes (5S and 18S ribosomal genes), and telomeric (TTAGGG)n sequences. The diploid number of the species was 2n = 48, with heterochromatic blocks in the centromeric and pericentromeric regions, as well as distal signals; the nucleolus organizer regions (NORs) were associated with the heterochromatic region. The 18S and 5S recombinant DNA (rDNA) clusters were located in the distal region of chromosome pairs 1 and 11, respectively. The similarities of the karyotype macrostructure found among the centropomid species reinforce their exceptional chromosomal stability. However, the presence of heterochromatic blocks and location of NORs suggest the occurrence of structural rearrangements, which indicates that evolutionary dynamics at the microstructural level in this group may be relatively complex and should be evaluated carefully in any study that targets the production of hybrids for aquaculture.

The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants

One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that the directionality of their reduced chromosome number was through large structural rearrangements. A series of structural rearrangements were identified comparing the de novo G. kirkii genome sequence to genome sequences of Gossypium, including chromosome fusions and inversions. Genome comparison between G. kirkii and Gossypium suggests that multiple steps are required to generate the extant structural differences.

The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate

Constitutive genomes of allopolyploid species evolve throughout their life span. However, the consequences of long-term alterations on the interdependency between each original genome have not been established. Here, we attempted an approach corresponding to subgenome extraction from a previously sequenced natural allotetraploid, offering a unique opportunity to evaluate plant viability and structural evolution of one of its diploid components. We employed two different strategies to extract the diploid AA component of the Brassica napus variety 'Darmor' (AACC, 2n = 4x = 38) and we assessed the genomic structure of the latest AA plants obtained (after four to five rounds of selection), using a 60K single nucleotide polymorphism Illumina array. Only one strategy was successful and the diploid AA plants that were structurally characterized presented a lower proportion of the B. napus A subgenome extracted than expected. In addition, our analyses revealed that some genes lost in a polyploid context appeared to be compensated for plant survival, either by conservation of genomic regions from B. rapa, used in the initial cross, or by some introgressions from the B. napus C subgenome. We conclude that as little as c. 7500 yr of coevolution could lead to subgenome interdependency in the allotetraploid B. napus as a result of structural modifications.

Plastome Evolution in Hemiparasitic Mistletoes

Santalales is an order of plants consisting almost entirely of parasites. Some, such as Osyris, are facultative root parasites whereas others, such as Viscum, are obligate stem parasitic mistletoes. Here, we report the complete plastome sequences of one species of Osyris and three species of Viscum, and we investigate the evolutionary aspects of structural changes and changes in gene content in relation to parasitism. Compared with typical angiosperms plastomes, the four Santalales plastomes are all reduced in size (10–22% compared with Vitis), and they have experienced rearrangements, mostly but not exclusively in the border areas of the inverted repeats. Additionally, a number of protein-coding genes (matK, infA, ccsA, rpl33, and all 11 ndh genes) as well as two transfer RNA genes (trnG-UCC and trnV-UAC) have been pseudogenized or completely lost. Most of the remaining plastid genes have a significantly changed selection pattern compared with other dicots, and the relaxed selection of photosynthesis genes is noteworthy. Although gene loss obviously reduces plastome size, intergenic regions were also shortened. As plastome modifications are generally most prominent in Viscum, they are most likely correlated with the increased nutritional dependence on the host compared with Osyris.

Changes in protein structure and dynamics as a function of hydration from (1)H second moments

We report the proton second moment obtained directly from the Free Induction Decay (FID) of the NMR signal of variously hydrated bovine serum albumin (BSA) and hen egg white lysozyme (HEWL) and from the width of the NMR Z-spectrum of the cross-linked protein gels of different concentrations. The second moment of the proteins decreases in a continuous stepwise way as a function of increasing water content, which suggests that the structural and dynamical changes occur in small incremental steps. Although the second moment is dominated by the short range distances of nearest neighbors, the changes in the second moment show that the protein structure becomes more open with increasing hydration level. A difference between the apparent liquid content of the sample as found from decomposition of the FID and the analytically determined water content demonstrates that water absorbed in the early stages of hydration is motionally immobilized and magnetically indistinguishable from rigid protein protons while at high hydration levels some protein side-chain protons move rapidly contributing to liquid-like component of the NMR signal.