Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution

Supplementary_data.zip

These files are supplementary data for the Research article "Three de novo assembled wild cacao genomes from Upper Amazon reveal new insights into an early divergence of chocolate trees" Orestis Nousias1,*, Jinfang Zheng1,*, Tang Li1, Lyndel W Meinhardt2, Bryan Bailey2, Osman Gutierrez3, Stephen P. Cohen2, Dapeng Zhang2,#, Yanbin Yin1,# 1Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA 2U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA 3U.S. Department of Agriculture, Subtropical Horticulture Research Station, Miami, FL, USA *co-first authors #corresponding authors Yanbin Yin   Tel: 1-402-472-4303 Email: [email protected] Dapeng Zhang Tel: 1-301-504-7477 Email: [email protected] The article is not yet submitted to a journal</p

Development and application of genetic tools aiming at the future production improvement in two new species for the mediterranean aquacultiure, the meagre (Argyrosomus regius) and the greater amberjack (Seriola dumerili)

The development of new genetic tools, as well as the optimal use of existing ones to improve production in fish farming for Meagre and Greater amberjack species has been the main research goal in this doctoral dissertation. Modernization in the design of breeding programs as well as genetic selection assisted by polymorphic markers, are conditions which in their implementation give important possibilities in the production process. We developed two multiplex genetic loci for Meagre and Greater amberjack, respectively, which we used to estimate the genetic diversity of 11 stocks consisting of 946 farmed fish, to investigate the effects of stock mixing and the resulting genetic clustering via population genetics parameters. We proposed a methodology for estimating kinship relationships in multiple stocks, based on which we estimated individual inbreeding values, and we compared two methods of selecting broodstock from crosses of 27 parents from one stock. In addition, we investigated the heritability for the characters weight and length in Meagre, the genetic and phenotypic correlations of weight and length as well as the variation in the contribution of the offspring from a generation of 800 offspring to the formation of F1 families depending on effective population size. The detection of constituent elements of the genome of a species together with the description of the genetic base of important characters can contribute to the conservation of the species and the broadening of the possibilities of its productive utilization. A genetic linkage map for a species highlights genome evolution, facilitates trait mapping through QTL analysis, and improves genome assembly. We used a reduced genomic representation technique by creating a ddRAD library for six F1 families in the Meagre in a total of 266 fish, to construct a high density genetic map consisting of 4529 polymorphic SNP markers. We performed QTL analysis for weight and length, which detected a statistically significant QTL in linkage group 15. The genetic map was used for comparative genomic analysis, by finding homologs, in five genomes of teleost fish and showed a conserved evolutionarily karyotype structure in the Meagre. The observed syntenies, converged with published data, on the evolutionary proximity of the Scianidae family with the Sparidae family and specifically with the seabream, with the Moronidae family and the seabass, detected possible chromosomal rearrangement in the Meagre and especially in linkage group 17. In its entirety the dissertation provided with new genetic tools for the Meagre and Greater amberjack for the design of breeding programs. Furthermore, the first genetic linkage map of the Meagre from NGS data was contructed which was used for the genetic appreciation of the growth-related characters weight and length in the Meagre, presents with elements of evolution of the Meagre genome, and provides a high-density genetic map as a valuable tool for research and production.Η ανάπτυξη νέων γενετικών εργαλείων, όπως και η βέλτιστη χρήση των υπαρχόντων για την βελτίωση της παραγωγής στην ιχθυοκαλλιέργεια για τα είδη Κρανιό και Μαγιάτικο υπήρξε ο κεντρικός ερευνητικός στόχος στην παρούσα διδακτορική διατριβή. Ο εκσυγχρονισμός στον σχεδιασμό των προγραμμάτων αναπαραγωγής καθώς και η γενετική επιλογή υποβοηθούμενη από πολυμορφικούς δείκτες, είναι προϋποθέσεις οι οποίες στην υλοποίηση τους δίνουν σημαντικές δυνατότητες στην παραγωγική διαδικασία. Αναπτύξαμε δύο multiplex γενετικών τόπων για τον Κρανιό και το Μαγιάτικο, αντίστοιχα, τα οποία χρησιμοποιήσαμε για την εκτίμηση της γενετικής παραλλακτικότητας 11 αποθεμάτων αποτελούμενων από 946 ιχθύες σε συνθήκες εκτροφής, για την διερεύνηση των συνεπειών της ανάμιξης αποθεμάτων καθώς και της προκύπτουσας γενετικής ομαδοποίησης μέσω παραμέτρων πληθυσμιακής γενετικής. Προτείναμε μία μεθοδολογία εκτίμησης σχέσεων συγγένειας σε πολλαπλά αποθέματα, με βάση την οποία εκτιμήσαμε ατομικούς συντελεστές ενδογαμίας, όπως επίσης συγκρίναμε δύο μεθόδους επιλογής γεννητόρων από διασταυρώσεις 27 γονέων από ένα απόθεμα. Επιπρόσθετα, διερευνήσαμε την κληρονομησιμότητα για τους χαρακτήρες βάρος και μήκος στον Κρανιό, τις γενετικές και φαινοτυπικές συσχετίσεις βάρους και μήκους καθώς και την διακύμανση στην συνεισφορά των γεννητόρων από μία γέννα 800 απογόνων στην διαμόρφωση των F1 οικογενειών σε συνάρτηση με το δραστικό μέγεθος πληθυσμού. Η ανίχνευση στοιχείων συγκρότησης του γονιδιώματος ενός είδους μαζί με την περιγραφή της γενετικής βάσης σημαντικών χαρακτήρων μπορεί να συνεισφέρει στην διατήρηση του είδους και στις δυνατότητες παραγωγικής του αξιοποίησης. Ένας γενετικός χάρτης σύνδεσης για ένα είδος, αναδεικνύει στοιχεία εξέλιξης του γονιδιώματος, διευκολύνει την χαρτογράφηση χαρακτήρων μέσω της εύρεσης QTL, και βελτιώνει την συναρμολόγηση του γονιδιώματος. Χρησιμοποιήσαμε μία τεχνική μειωμένης γονιδιωματικής εκπροσώπησης μέσω της δημιουργίας βιβλιοθήκης ddRAD για έξι F1 οικογένειες στον Κρανιό σε ένα σύνολο 266 ιχθύων, για την κατασκευή γενετικού χάρτη υψηλής πυκνότητας αποτελούμενο από 4529 πολυμορφικούς SNP δείκτες. Διεξαγάγαμε ανάλυση QTL για το βάρος και το μήκός, η οποία ανίχνευσε ένα στατιστικό σημαντικά QTL στο linkage group 15. Ο γενετικός χάρτης χρησιμοποιήθηκε για την συγκριτική γονιδιωματική ανάλυση, μέσω εύρεσης ομολογιών, σε πέντε γονιώματα τελεόστεων ιχθύων και ανέδειξε έναν μία εξελικτικά συντηρημένη δομή του καρυοτύπου στον Κρανιό. Οι παρατηρούμενες συντενίες, συνέκλιναν με δημοσιευμένα δεδομένα για την κοντινή εξελικτικά απόσταση της οικογένειας Scianidae με την οικογένεια Sparidae και συγκεκριμένα με την τσιπούρα, με την οικογένεια Moronidae και το λαβράκι, ανίχνευσαν πιθανές χρωμοσωμικές αναδιατάξεις στον Κρανιό και είδικά στο linkage group 17. Η διατριβή παρέχει στο σύνολο της, νέα γενετικά εργαλεία για τον Κρανιό και Μαγιάτικο για τον σχεδιασμό προγραμμάτων αναπαραγωγής, τον πρώτο γενετικό χάρτη σύνδεσης στον Κρανιό προερχόμενο από NGS δεδομένα, για πρώτη φορά ανιχνεύει την γενετική βάση των αναπτυξιακών χαρακτήρων βάρος και μήκος στον Κρανιό, παρουσιάζει για πρώτη φορά στοιχεία εξέλιξης του γονιδιώματος του Κρανιού, και παρέχει έναν υψηλής πυκνότητας γενετικό χάρτη ως ένα πολύτιμο εργαλείο για την έρευνα και την παραγωγή

Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes

This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes

Parentage assignment, estimates of heritability and genetic correlation for growth-related traits in meagre Argyrosomus regius

Meagre is a relatively new aquaculture species with great potential in large scale European aquaculture. The primary objective of the study was to describe, for the first time, parentage allocation and assign offspring to their parents for an industrial scale production system. A total of 800 meagre fish were sampled from two large cages in January and May 2016, both part of a commercial farm site in Valencia, Spain. All fish originated from the same spawning event obtained from a broodstock of 6 females and 13 males. However, due to differential growth during the juvenile stage the fish were graded into two groups, a group of larger juveniles that was transferred to one cage (batch 1) and a group of smaller juveniles that were transferred to the second cage (batch 2). Total length and weight was measured for all fish that were genotyped with a 10 microsatellite loci multiplex to infer parentage based on parental genotypes. Parentage assignment rate was high (87.5% for batch 1 and 95% for batch 2) and provided evidence that offspring belonged to 20 families. Half of the broodstock was identified as probable parents of the offspring (five females and seven males).Between the two sea-cages, a slight differential composition for the same families was encountered. The fifteen shared families that the offspring were assigned to, were analyzed for statistical significant differences concerning body weight and total body length, differences which were observed in 3 families for both batches. We estimated the heritability for body weight and total body length, as well as the genetic and phenotypic correlations for these two traits. Batch 1 showed higher heritability estimates than batch 2 with the genetic and phenotypic correlation estimates being almost the same for both batches. Certain parents contributed more offspring and exhibited dominance in spawning. Similarly, the growth related traits of body weight and total body length of the dominant parents correlate, putatively, with the statistical important differences that are observed in these three families.info:eu-repo/semantics/acceptedVersio

The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of <i>Magnoliales</i>, and a Putative Gene Cluster for Acetogenin Biosynthesis

Annona cherimola (cherimoya) is a species renowned for its delectable fruit and medicinal properties. In this study, we developed a chromosome-level genome assembly for the cherimoya ‘Booth’ cultivar from the United States. The genome assembly has a size of 794 Mb with a N50 = 97.59 Mb. The seven longest scaffolds account for 87.6% of the total genome length, which corresponds to the seven pseudo-chromosomes. A total of 45,272 protein-coding genes (≥30 aa) were predicted with 92.9% gene content completeness. No recent whole genome duplications were identified by an intra-genome collinearity analysis. Phylogenetic analysis supports that eudicots and magnoliids are more closely related to each other than to monocots. Moreover, the Magnoliales was found to be more closely related to the Laurales than the Piperales. Genome comparison revealed that the ‘Booth’ cultivar has 200 Mb less repeats than the Spanish cultivar ‘Fino de Jete’, despite their highly similar (>99%) genome sequence identity and collinearity. These two cultivars were diverged during the early Pleistocene (1.93 Mya), which suggests a different origin and domestication of the cherimoya. Terpene/terpenoid metabolism functions were found to be enriched in Magnoliales, while TNL (Toll/Interleukin-1-NBS-LRR) disease resistance gene has been lost in Magnoliales during evolution. We have also identified a gene cluster that is potentially responsible for the biosynthesis of acetogenins, a class of natural products found exclusively in Annonaceae. The cherimoya genome provides an invaluable resource for supporting characterization, conservation, and utilization of Annona genetic resources

Three <i>de novo</i> assembled wild cacao genomes from the Upper Amazon region

Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. In this study, we constructed three high-quality chromosome-level genomes,de novoassembled using long reads sequencing and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of wild cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. We found that the five cacao genetic clusters diverged in the early and middle Pleistocene period, approximately 1.83 – 0.69 million years ago. This finding challenges the existing Pleistocene refugia hypothesis that suggests a more recent cacao intra-specific diversification. We also found significantly higher percentages of transposable elements and lower numbers of disease resistance genes in the wild cacao genomes than in the domesticated reference genomes. Our results serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying cacao genetic diversity.</p

Genomes of multicellular algal sisters to land plants illuminate signaling network evolution.

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution