Development and characterization of non-coding RNA-derived simple sequence repeat markers in coconut (Cocos nucifera L.).

Non-coding RNA (ncRNA)-based SSR markers are highly useful in molecular breeding as ncRNAs play a significant role in gene regulation. In the present study, for the first time in coconut, we have identified 597 ncRNA-derived SSR markers, including 509 long non-coding RNASSRs (lncRNASSRs) and 88 micro RNASSRs (miRNASSRs). Of these, 20 primers (10 each from lncRNA-SSR and miRNA-SSR) were selected, screened on 6 coconut accessions, and 50% produced polymorphic fragments. These 10 polymorphic primers were used for genotyping 96 palms of 16 coconut accessions, comprising eight tall and dwarf accessions each. The number of alleles ranged from 2 to 9 per SSR marker, with an average of 4.6 alleles per locus. The average heterozygosity and Shannon index were 0.5 and 1.1, respectively, suggesting that ncRNA-SSRs show high polymorphism level. Distance-based cluster analyses revealed that all the tall and dwarf accessions were differentiated and grouped in different clusters. The study demonstrates the usefulness of ncRNA-based SSR markers for assessing genetic diversity and genetic improvement in coconut.

The complete chloroplast genome data of Areca catechu (Arecaceae).

Areca is a genus comprising about 50 species endemic to the humid tropics. Arecanut (Areca catechu L.) is a commercially and economically important crop in South and Southeast Asia. In addition to its contribution to the agricultural economies of countries where the crop is grown, arecanut holds an important place in the religious, cultural, and social milieu of the rural folks. The nuts have been used since time immemorial in traditional Indian (Unani and Ayurveda) and Chinese herbal systems of medicine for the treatment of various disorders like rheumatism, parasitic infection, diseases of gastrointestinal tracts, and depression. Here, we report the complete chloroplast (cp) genome sequence of arecanut. The cp genome of A. catechu was a typical circular DNA molecule with a size of 158,689 bp in length. The genome possessed a typical quadripartite structure composed of a pair of inverted repeats (IRa and IRb) of 27,137 bp separated by a large single-copy (LSC) region of 86,814 bp and a small single-copy (SSC) region of 17,601 bp and a GC content of 37.3%. The cp genome of arecanut encodes a set of 133 genes, comprising 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes; among these, 21 contained introns. A total of 70 SSR loci were detected, the majority being in inter-genic regions. Phylogenetic analysis revealed that A. catechu was closely related to A. vestiaria.

Development of EST-SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.).

Genetic improvement in coconut relies on exploiting the vast existing diversity among coconut accessions. Robust molecular markers are a pre-requisite for efficient characterization of genetic diversity. Microsatellites or simple sequence repeats (SSRs), mined from expressed sequence tags (ESTs), constitute an important resource for analysis of genetic diversity as they are abundant, polymorphic and represent function regions of the genome. We have identified a total of 318,528 putative EST-SSRs from 130,942 unigenes utilizing a leaf transcriptome dataset of coconut. Among the EST-SSRs, dinucleotide repeats were abundant (219,912; 69.04%) followed by trinucleotide (70,722; 22.2%) and tetra-nucleotide repeats (6281; 1.9%). Among the dinucleotide repeat motifs, the dominant repeat was AG/CT (35.87%), followed by AT/AT (18.59%), while the dominant trinucleotide repeat was AAG/CTT (4.59%). One hundred and twenty EST-SSR primer pairs were designed and utilized to amplify six DNA samples of coconut accessions. Fifty primers (41.7%) produced reproducible polymorphic fragments of expected sizes, from which a total of 10 primers were selected for the diversity assessment in 186 palms of 50 coconut accessions, comprising of 25 each of tall and dwarf accessions. A total of 137 alleles were detected with an average of 13.7 alleles per SSR locus. The number of alleles observed at each locus in the data set ranged from 7 to 22. All the loci showed 100% polymorphism with respect to the samples screened. The average observed heterozygosity was 0.46. The PIC values ranged from 0.79 (CnKGDEST129 and CnKGDEST100) to 0.91 (CnKGDEST117 and CnKGDEST122) with a mean value of 0.85, indicating the capacity of the EST-SSR markers to detect high levels of polymorphism. The cluster analysis revealed that accessions were generally clustered based on their relative similarity and irrespective of their geographic origins. The present study demonstrates the usefulness of transcriptome sequencing as a rapid and cost-effective methodology for the development of molecular markers. The EST-SSR markers generated through this study constitute useful and reliable tools for assessment of genetic diversity and marker-assisted selection in coconut.

Dataset of dual RNA-sequencing of Phytophthora palmivora infecting coconut (Cocos nucifera L.).

Phytophthora spp. is an oomycetes pathogen which causes serious damage to a wide range of crops. Bud rot disease of coconut palm, caused by P. palmivora, causes huge economic losses since it cannot be detected at an early stage. Utilizing dual RNA-sequencing (RNA-seq), we have simultaneously investigated the gene expression patterns in both, the infecting oomycete (P. palmivora) and infected host (coconut leaflets). Samples were collected at three time points viz., 12, 24 and 36 h, from both infected and uninfected (control) tissues and subjected to RNA-seq on an Illumina Hiseq™ 2500 sequencing platform. High quality reads obtained were subjected to mapping with corresponding reference genomes by using the HISAT2/ StringTie package. A total of 81,683 transcripts were generated against the coconut reference genome, while 9340 transcripts were generated against P. palmivora genome. Out of these, a total of 64,639 coconut transcripts and 9168 P. palmivora transcripts could be annotated using BLASTx. Gene ontology (GO) analysis, carried out using Blast2GO, resulted in 212,643 coconut and 30,736 P palmivora transcripts being functionally classified, with a single gene product described by numerous terms under the three classifications. The insights obtained could contribute to an understanding of pathogenesis of P. palmivora and inducible defense response of coconut leaves to P. palmivora.