De Novo Genome Sequence Assembly of Dwarf Coconut (Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species

Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf

The high-quality genome of coconut (Cocos nucifera L.) is a crucial resource for enhancing agronomic traits and studying genome evolution within the Arecaceae family. We sequenced the Chowghat Green Dwarf cultivar, which is resistant to the root (wilt) disease, utilizing Illumina, PacBio, ONT, and Hi-C technologies to produce a chromosome-level genome of ~ 2.68 Gb with a scaffold N50 of 174 Mb; approximately 97% of the genome could be anchored to 16 pseudo-molecules (2.62 Gb). In total, 34,483 protein-coding genes were annotated; the BUSCO completeness score was 96.80%, while the k-mer completeness was ~ 87%. The assembled genome includes 2.19 Gb (81.64%) of repetitive sequences, with long terminal repeats (LTRs) constituting the most abundant class at 53.76%. Additionally, our analysis confirms two whole-genome duplication (WGD) events in the C. nucifera lineage. A genome-wide analysis of LTR insertion time revealed ancient divergence and proliferation of copia and gypsy elements. In addition, 1368 RGAs were discovered in the CGD genome. We also developed a web server 'Kalpa Genome Resource' ( http://210.89.54.198:3000/ ), to manage and store a comprehensive array of genomic data, including genome sequences, genetic markers, structural and functional annotations like metabolic pathways, and transcriptomic profiles. The web server has an embedded genome browser to analyze and visualize the genome, its genomics elements, and transcriptome data. The in-built BLAST server allows sequence homology searches against genome, annotated transcriptome & proteome sequences. The genomic dataset and the database will support comparative genome analysis and can expedite genome-driven breeding and enhancement efforts for tapping genetic gains in coconut.

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Nypa fruticans (Wurmb), a mangrove palm species with origins dating back to the Late Cretaceous period, is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms. Here, we present a chromosome-level genome sequence and assembly for N. fruticans. We integrated the genomes of N. fruticans and other palm family members for a comparative genomic analysis, which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago, shaping the distinctive characteristics observed in this clade. We also inferred a low mutation rate for the N. fruticans genome, which underwent strong purifying selection and evolved slowly, thus contributing to its stability over a long evolutionary period. Moreover, ancient duplicates were preferentially retained, with critical genes having experienced positive selection, enhancing waterlogging tolerance in N. fruticans. Furthermore, we discovered that the pseudogenization of Early Methionine-labelled 1 (EM1) and EM6 in N. fruticans underly its crypto-vivipary characteristics, reflecting its intertidal adaptation. Our study provides valuable genomic insights into the evolutionary history, genome stability, and adaptive evolution of the mangrove palm. Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation

Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.

A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation

The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African oil palm (Elaeis guineensis) is one of the most important palms. However, the genome sequences of palms that are currently available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm, Dura, assembled by integrating long reads with ∼ 150× genome coverage. The assembled genome was 1.7 Gb in size, covering 94.5% of the estimated genome, of which 91.6% was assigned into 16 pseudochromosomes and 73.7% was repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons, following the last whole-genome duplication, likely explains the genome size variation across palms. Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors. Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma. Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut

Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. Unfortunately, the sustainable growth of the coconut industry has been hampered due to a shortage of good quality seedlings. Genetic improvement through the traditional breeding approach faced considerable obstacles due to its perennial nature, protracted juvenile period, and high heterozygosity. Molecular biotechnological tools, including molecular markers and next-generation sequencing (NGS), could expedite genetic improvement efforts in coconut. Researchers have employed various molecular markers to reveal genetic diversity among coconut populations and for the construction of a genetic map for exploitation in coconut breeding programs worldwide. Whole genome sequencing and transcriptomics on the different varieties have generated a massive amount of publicly accessible sequence data, substantially improving the ability to analyze and understand molecular mechanisms affecting crop performance. The production of high-yielding and disease-resilient coconuts and the deciphering of the complex coconut genome's structure can profit tremendously from these technologies. This paper aims to provide a comprehensive review of the progress of coconut research, using genomics, transcriptomics, and molecular markers initiatives.

Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits

Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms' importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population's demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.

Improving Coconut Using Modern Breeding Technologies: Challenges and Opportunities

Coconut (Cocos nucifera L.) is a perennial palm with a wide range of distribution across tropical islands and coastlines. Multitude use of coconut by nature is important in the socio-economic fabric framework among rural smallholders in producing countries. It is a major source of income for 30 million farmers, while 60 million households rely on the coconut industry directly as farm workers and indirectly through the distribution, marketing, and processing of coconut and coconut-based products. Stagnant production, inadequate planting materials, the effects of climate change, as well as pests and diseases are among the key issues that need to be urgently addressed in the global coconut industry. Biotechnology has revolutionized conventional breeding approaches in creating genetic variation for trait improvement in a shorter period of time. In this review, we highlighted the challenges of current breeding strategies and the potential of biotechnological approaches, such as genomic-assisted breeding, next-generation sequencing (NGS)-based genotyping and genome editing tools in improving the coconut. Also, combining these technologies with high-throughput phenotyping approaches and speed breeding could speed up the rate of genetic gain in coconut breeding to solve problems that have been plaguing the industry for decades.

Genomic and Bioinformatic Resources for Perennial Fruit Species

In the post-genomic era, data management and development of bioinformatic tools are critical for the adequate exploitation of genomics data. In this review, we address the actual situation for the subset of crops represented by the perennial fruit species. The agronomical singularity of these species compared to plant and crop model species provides significant challenges on the implementation of good practices generally not addressed in other species. Studies are usually performed over several years in non-controlled environments, usage of rootstock is common, and breeders heavily rely on vegetative propagation. A reference genome is now available for all the major species as well as many members of the economically important genera for breeding purposes. Development of pangenome for these species is beginning to gain momentum which will require a substantial effort in term of bioinformatic tool development. The available tools for genome annotation and functional analysis will also be presented.

Mining and validation of novel simple sequence repeat (SSR) markers derived from coconut (Cocos nucifera L.) genome assembly

BACKGROUND

In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSRs are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers.

RESULTS

A total of 7139 novel SSR markers were derived from the genome assembly of coconut 'Catigan Green Dwarf' (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. The OligoAnalyzer tool was also employed using the following desired parameters: %GC, 40-60%; minimum ΔG value for hairpin loop, -0.3 kcal/mol; minimum ΔG value for self-dimer, -0.9 kcal/mol; and minimum ΔG value for heterodimer, -0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using 'Catigan Green Dwarf' (CATD), 'Laguna Tall' (LAGT), 'West African Tall' (WAT), and SYNVAR (LAGT × WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes.

CONCLUSION

The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.

Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing

Background

The Philippines is among the top 10 major exporters of mango worldwide. However, genomic studies of Philippine mangoes remain largely unexplored and lacking. Here, we sequenced the whole genome of the three Philippine mango species, namely, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica “Carabao” variety using Illumina HiSeq 2500, to identify and analyze their genome-wide variants (SNPs and InDels).

Results

The high confidence variants were identified by successfully mapping 93–95% of the quality-filtered reads to the Alphonso and Tommy Atkins mango reference genomes. Using these two currently available mango genomes, most variants were observed in M. odorata (4,353,063 and 4,277,287), followed by M. altissima (3,392,763 and 3,449,917), and lastly, M. indica Carabao (2,755,267 and 2,852,480). Approximately 50, 46, and 38% of the variants were unique in the three Philippine mango genomes. The analysis of variant effects and functional annotation across the three mango species revealed 56,982 variants with high-impact effects mapped onto 37,746 genes, of which 25% were found to be novel. The affected mango genes include those with potential economic importance such as 6945 genes for defense/resistance/immune response, 323 genes for fruit development, and 338 genes for anthocyanin production.

Conclusions

To date, this is the first sequencing effort to comprehensively analyze genome-wide variants essential for the development of genome-wide markers specific to these mango species native to the Philippines. This study provides an important genomic resource that can be used for the genetic improvement of mangoes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00326-3.

Genome-wide diversity analysis to infer population structure and linkage disequilibrium among Colombian coconut germplasm

Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) with the goal of analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diverse coconut panel consisting of 112 coconut accessions from the Atlantic and Pacific coasts of Colombia. A comprehensive catalog of approximately 40,000 SNPs with a minor allele frequency (MAF) of > 0.05 is presented. A total of 40,614 SNPs were found but only 19,414 anchored to chromosomes. Of these, 10,338 and 4606 were exclusive to the Atlantic and Pacific gene pools, respectively, and 3432 SNPs could differentiate both gene pools. A filtered subset of unlinked and anchored SNPs (1271) showed a population structure at K = 4, separating accessions from the Pacific and Atlantic coasts that can also be distinguished by palm height, as found in previous studies. The Pacific groups had a slow LD decay, low Fixation Index (Fst) and low nucleotide diversity (π), while the Atlantic group had slightly higher genetic diversity and faster LD decay. Genome-wide diversity analyses are of importance to promote germplasm conservation and breeding programs aimed at developing new cultivars better adapted to the region.

Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)

BACKGROUND

Durian (Durio zibethinus L.) is a tropical fruit crop which is popular in Southeast Asia but recently gaining popularity in other parts of the world. In this study, we analyzed the resistance gene analogs (RGAs) of durian through mining of the currently available reference genome of its 'Musang King' cultivar (PRJNA400310).

RESULTS

A total of 2586 RGAs were identified in the durian genome consisting of 47 nucleotide binding site proteins (NBS), 158 NBS-leucine rich repeat proteins (NL), 400 coiled-coil NBS-LRR (CNL), 72 toll/interleukin-1 receptor NBS-LRR (TNL), 54 coiled-coil NBS (CN), 10 toll/interleukin-1 receptor NBS (TN), 19 toll/interleukin-1 receptor with unknown domain (TX), 246 receptor-like proteins (RLP), 1,377 receptor-like kinases (RLK), 185 TM-CC, and 18 other NBS-containing proteins with other domains. These RGAs were functionally annotated and characterized via gene ontology (GO) analysis. Among the RGAs with the highest copies in durian genome include the putative disease resistance RPP13-like protein 1, disease resistance protein At4g27190, disease resistance protein RPS6, Probable disease resistance protein At4g27220, and putative disease resistance protein RGA3, while 35 RGAs were found to be novel. Phylogenetic analyses revealed that the genome-wide RGAs were broadly clustered into four major clades based on their domain classification.

CONCLUSION

To our knowledge, this is the most comprehensive analysis of durian RGAs which provides a valuable resource for genetic, agronomic, and other biological research of this important tropical fruit crop.

Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection

Optical mapping plays an important role in plant genomics, particularly in plant genome assembly and large-scale structural variation detection. While DNA sequencing provides base-by-base nucleotide information, optical mapping shows the physical locations of selected enzyme restriction sites in a genome. The long single-molecule maps produced by optical mapping make it a useful auxiliary technique to DNA sequencing, which generally cannot span large and complex genomic regions. Although optical mapping, therefore, offers unique advantages to researchers, there are few dedicated tools to assist in optical mapping analyses. In this chapter, we present runBNG2, a successor of runBNG to help optical-mapping data analysis for diverse datasets.

Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species

Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.

Frequent Gene Duplication/Loss Shapes Distinct Evolutionary Patterns of NLR Genes in Arecaceae Species

Nucleotide-binding leucine-rich repeat (NLR) genes play a key role in plant immune responses and have co-evolved with pathogens since the origin of green plants. Comparative genomic studies on the evolution of NLR genes have been carried out in several angiosperm lineages. However, most of these lineages come from the dicot clade. In this study, comparative analysis was performed on NLR genes from five Arecaceae species to trace the dynamic evolutionary pattern of the gene family during species speciation in this monocot lineage. The results showed that NLR genes from the genomes of Elaeis guineensis (262), Phoenix dactylifera (85), Daemonorops jenkinsiana (536), Cocos nucifera (135) and Calamus simplicifolius (399) are highly variable. Frequent domain loss and alien domain integration have occurred to shape the NLR protein structures. Phylogenetic analysis revealed that NLR genes from the five genomes were derived from dozens of ancestral genes. D. jenkinsiana and E. guineensis genomes have experienced “consistent expansion” of the ancestral NLR lineages, whereas a pattern of “first expansion and then contraction” of NLR genes was observed for P. dactylifera, C. nucifera and C. simplicifolius. The results suggest that rapid and dynamic gene content and structure variation have shaped the NLR profiles of Arecaceae species.

High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height

BACKGROUND

Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants.

RESULTS

Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2-8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47-53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf.

CONCLUSION

We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.

Cloning Coconut via Somatic Embryogenesis: A Review of the Current Status and Future Prospects

Coconut [Cocos nucifera L.] is often called "the tree of life" because of its many uses in the food, beverage, medicinal, and cosmetic industries. Currently, more than 50% of the palms grown throughout the world are senile and need to be replanted immediately to ensure production levels meet the present and increasing demand for coconut products. Mass replanting will not be possible using traditional propagation methods from seed. Recent studies have indicated that in vitro cloning via somatic embryogenesis is the most promising alternative for the large-scale production of new coconut palms. This paper provides a review on the status and prospects for the application of somatic embryogenesis to mass clonal propagation of coconut.

Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote)

BACKGROUND AND AIMS

The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication.

METHODS

We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material.

KEY RESULTS

A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose.

CONCLUSIONS

The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.

Transcriptome analysis reveals key defense-related genes upon SA induction in Cocos nucifera L

BACKGROUND

Salicylic acid (SA) is an important regulator of genes involved in plant defense and pathogen-triggered systemic acquired resistance (SAR). Coconut is an important crop affected by several pathogens. Reported evidence suggests SA involvement in defense responses, including SAR in coconut.

OBJECTIVE

To identified differentially expressed genes in leaf and root tissues of coconut plantlets, as a result of SA, that might be involved in coconut defense responses.

METHODS

Comparative transcriptomic analysis by RNA-Seq of leaf and root tissues from in vitro coconut plantlets unexposed and exposed to SA 2.5 mM for 48 h. And in silico validation of gene expression by qRT-PCR.

RESULTS

We identified 4615 and 3940 differentially expressed unigenes (DEUs) in leaf and root tissues respectively. Our GO analysis showed functional categories related to the induction of defense responses, such as "systemic acquired resistance" and highly enriched hormone categories, such as abscisic acid. The most abundant KEGG pathway in our results was "Biosynthesis of antibiotics". Our findings support that exogenous application of SA to plantlets induced the activation of PRs, RGAs, ICS2, NLTP2, PER4, TRXM and some WRKYs mediated by NPR1-dependent pathways. Also, we found DEUs, such as BZR1, HSL1, and WHY2 that support that SA could regulate defense-related genes through NPR1-independent pathways.

CONCLUSION

The present study of massive data analysis carried out on coconut plantlets exposed to SA, generates valuable information that increases our understanding of defense molecular mechanisms in coconut and open new venues for research for the improvement of management of coconut diseases.

Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance

Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n = 32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community.

Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand

Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) mining from a high-throughput genotyping-by-sequencing (GBS) study of a collection of 38 coconut accessions. A total of 22,748 SSRs with di-, tri-, tetra-, penta- and hexanucleotide repeats of five or more were identified, 2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions, and 315 loci were suitable for the development of SSR markers. One hundred loci were selected, and primer pairs for each SSR locus were designed and validated in 40 coconut accessions. The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus, with an average of 3.01 alleles. The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure, principal coordinate analysis (PCoA), and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand. The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding. The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome.