<i>De Novo</i> Genome Sequence Assembly of Dwarf Coconut (<i>Cocos nucifera</i> L. ‘Catigan Green Dwarf’) Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species

Lantican, Darlon V.; Strickler, Susan R.; Canama, A.O.; Gardoce, Roanne R.; Mueller, Lukas A.; Galvez, H.F.

doi:10.1534/g3.119.400215

Cited by 61 publications

(56 citation statements)

References 130 publications

(178 reference statements)

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“…The most abundant class of SSRs identified from GBS sequences in this study was dinucleotide repeats. Similar results regarding abundant classes of coconut SSRs have been reported previously 42 . The most frequently identified type of dinucleotide repeat in the present study was AG/CT, similar to that identified for gene-based SRRs in a previous report 8 .…”

Section: Discussionsupporting

confidence: 91%

“…The most frequently identified type of dinucleotide repeat in the present study was AG/CT, similar to that identified for gene-based SRRs in a previous report 8 . However, this dinucleotide category was different from that identified from a whole-genome assembly, which was AT/TA 42 . Our newly developed SSR markers were tested for their effectiveness by using them to assess the genetic diversity of a collection of 40 coconut accessions.…”

Section: Discussioncontrasting

confidence: 68%

“…From these loci, 309 primer pairs were developed, 191 of which were polymorphic across a set of ten coconut accessions. Recently, a total of 7139 genome-wide SSR markers were designed on the basis of a whole-genome assembly of coconut 42 . However, the validation of these markers was not reported.…”

Section: Discussionmentioning

confidence: 99%

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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

et al. 2020

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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.

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Section: Discussionsupporting

confidence: 91%

Section: Discussioncontrasting

confidence: 68%

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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

et al. 2020

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“…The draft genome of a tall accession (Hainan Tall) has been made available (Xiao et al, 2017), with a scaffold length of 2.20 Gb (N50 = 418 kb). Also, while the analysis of the Chowghat Green Dwarf (CGD) genome was underway, the genome of a Catigan Green Dwarf, consisting of 2.1 Gb (N50 = 570.49 kb) sequence, has been published (Lantican et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Assembly and Annotation of the Nuclear and Organellar Genomes of a Dwarf Coconut (Chowghat Green Dwarf) Possessing Enhanced Disease Resistance

Muliyar

Chowdappa

Behera

et al. 2020

OMICS: A Journal of Integrative Biology

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Coconut (Cocos nucifera L.), an important source of vegetable oil, nutraceuticals, functional foods, and housing materials, provides raw materials for a repertoire of industries engaged in the manufacture of cosmetics, soaps, detergents, paints, varnishes, and emulsifiers, among other products. The palm plays a vital role in maintaining and promoting the sustainability of farming systems of the fragile ecosystems of islands and coastal regions of the tropics. In this study, we present the genome of a dwarf coconut variety ''Chowghat Green Dwarf'' (CGD) from India, possessing enhanced resistance to root (wilt) disease. Utilizing short reads from the Illumina HiSeq 4000 platform and long reads from the Pacific Biosciences RSII platform, we have assembled the draft genome assembly of 1.93 Gb. The genome is distributed over 26,855 scaffolds, with *81.56% of the assembled genome present in scaffolds of lengths longer than 50 kb. About 77.29% of the genome was composed of transposable elements and repeats. Gene prediction yielded 51,953 genes, which upon stringent filtering, based on Annotation Edit Distance, resulted in 13,707 genes, which coded for 11,181 proteins. Among these, we gathered transcript level evidence for a total of 6828 predicted genes based on the RNA-Seq data from different coconut tissues, since they presented assembled transcripts within the genome annotation coordinates. A total of 112 nucleotide-binding and leucine-rich repeat loci, belonging to six classes, were detected. We have also undertaken the assembly and annotation of the CGD chloroplast and mitochondrial genomes. The availability of the dwarf coconut genome shall prove invaluable for deducing the origin of dwarf coconut cultivars, dissection of genes controlling plant habit and fruit color, and accelerated breeding for improved agronomic traits.

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“…RGAs have been widely studied and efficiently used for breeding of resistant crops against insect pests and diseases (Karthika et al, 2019). One way to predict RGAs in plants is through bioinformatics analyses of next-generation sequencing (NGS) genomic and transcriptomic data (Lantican et al, 2019; Neupane et al, 2018; Zhang et al, 2016; Karthika et al, 2019). With the advent of this technology, it is possible to unravel gene networks and develop molecular markers tagging economically important traits, reveal other molecular information such as intron-exon boundaries and presence of transposable elements, and discover novel biological processes (Goodwin et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Lantican

Cortaga

Manohar

et al. 2020

Preprint

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10Plants have developed mechanisms to recognize pathogen and insect attacks and to 11 activate defense response against them through the action of resistance genes (R genes). 12Hence, R gene analogs (RGAs) have been widely studied and efficiently used for breeding of 13 resistant crops. Mango is an economic fruit crop largely cultivated in the (sub)tropics and thus, 14 is constantly challenged by a myriad of insect pests and diseases. RGAs of mango from 15 different varieties were identified and characterized via de novo assembly of raw transcriptome 16 sequences currently available in biological repositories. Using bioinformatics pipelines, a core 17 RGA database of mango with 747 protein models was established and were classified based 18 on their conserved domains and motifs: 53 nucleotide binding site protein (NBS); 27 nucleotide 19 binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 20 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 21 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like 22 proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein 23 (TM-CC), and 6 NBS-encoding proteins with other domains. Phylogenetic analysis broadly 24 clustered the core RGAs into 6 major clades based on their domain classification, while TM- 25CC formed subclades all across the tree. The phylogenetic results suggest highly divergent 26 functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms 27 race. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their 29 expression profiles across different mango varieties were also determined. From the mango 30 RGA transcripts, 134 unique EST-SSRs loci were identified, and primers were designed 31 targeting these potential markers. To date, this is the most comprehensive analysis of mango 32 RGAs which offer a trove of markers for direct utilization in resistance breeding of mango. 33 34 35 36 Introduction 37 Mango (Mangifera indica L.) is a globally popular fruit crop with economical and 38 agricultural significance, especially in the (sub)tropics where it is largely cultivated. One of the 39 constraints in mango production worldwide include a myriad of insect pests (e.g., oriental fruit 40 fly, mango hopper, cecid fly, etc.) and diseases, (e.g., anthracnose, stem-end rot, scab, etc.) 41 which can affect mango at different life stages thus significantly reducing fruit quality and yield 42 (Bally, 2006). These are major barriers to the export market and can impede international 43 trade as many pests and diseases in mango are important quarantine considerations. 44 Along the course of evolution, plants have generally developed mechanisms to 45 recognize pathogen and insect attacks and to activate defense response against them (Dangl 46 and Jones., 2001; Acevedo et al., 2015). The mole...

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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

Cited by 61 publications

References 130 publications

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

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

Assembly and Annotation of the Nuclear and Organellar Genomes of a Dwarf Coconut (Chowghat Green Dwarf) Possessing Enhanced Disease Resistance

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

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