Small cardamom genome: development and utilization of microsatellite markers from a draft genome sequence of Elettaria cardamomum Maton

Abstract

Small cardamom (Elettaria cardamomum Maton), the queen of spices, is the third most expensive spice in the world after saffron and vanilla, valued highly for its aroma and taste. This perennial herbaceous plant is a native of coastal parts of Southern India and displays a significant amount of morphological diversity. Its genetic potential has not been exploited due to lack of genomic resources limiting our understanding of the genome and important metabolic pathways which give it the economic advantage in the spice industry. Here, we report upon the de novo assembled, draft whole genome sequence of cardamom variety, Njallani Green Gold. We used a hybrid assembly strategy using the reads from the Oxford Nanopore, Illumina and 10x Genomics GemCode sequencing chemistries. The assembled genome length was 1.06 Gb (gigabases) which is close to the estimated genome size of cardamom. More than 75% of the genome was captured in 8000 scaffolds with a N50 of 0.15 Mb. The genome appears to have a high repeat content and 68055 gene models were predicted. The genome is close to Musa species and displays an expansion and contraction in different gene families. The draft assembly was used for in silico mining of simple sequence repeats (SSRs). A total of 2,50,571 SSRs were identified of which 2,18,270 were perfect SSRs and 32,301 were compound SSRs. Among the perfect SSRs, trinucleotides were most abundant (1,25,329) and hexanucleotide repeats appear least (2,380). From the 2,50,571 SSRs mined, 2,27,808 primer pairs were designed based on flanking sequence information. Wet lab validation was performed for 246 SSR loci and based on their amplification profiles, 60 SSR markers were used for diversity analysis of a set of 60 diverse cardamom accessions. The average number of alleles detected per locus were 14.57 with a minimum of 4 and maximum of 30 alleles. Population structure analysis revealed the presence of high degree of admixtures which could primarily be due to cross-pollination prevalent in this species. The SSR markers identified would help in the development of gene or trait-linked markers which can be subsequently used for marker-assisted breeding for crop improvement in cardamom. The information on utilization of the SSR loci for generation of markers has been developed into a public database, ‘cardamomSSRdb’ that is freely available for use by the cardamom community.

Construction of a Full-Length Transcriptome of Western Honeybee Midgut Tissue and Improved Genome Annotation

“…Here, using nanopore sequencing data from the midgut tissues, 17,345 SSRs were identified, with the greatest number being single-nucleotide repeats (11,616, 67.0%). This suggests that greater quantities and more types of SSRs were detected using long reads generated from nanopore sequencing, a result similar to the findings in other animals [ 11 , 60 , 61 ]. These increased SSR resources can establish a solid foundation for future studies on the conservation and genetic breeding of A. mellifera [ 62 ].…”

Testing the Genetic Variability of Turmeric (Curcuma longa L.) Genotypes through Simple Sequence Repeats Genomic-Based Microsatellite Markers

“…It is also recently concluded that the variability of turmeric could be due to the adaptability of genotypes to diverse climatic situations . It is also important to utilize the recent sequence information generated in the study of Gaikwad for developing the turmeric SSR marker database. In summary, the turmeric genotype CL 258 could be proposed for use in more than a few breeding programs, and it is suggested to be the suitable genotype for extensive farming by superior farmers.…”