Chloroplast microsatellite markers for <i>Artocarpus</i> (Moraceae) developed from transcriptome sequences

Gardner, Elliot M.; Laricchia, Kristen M.; Murphy, Matthew; Ragone, Diane; Scheffler, Brian E.; Simpson, Sheron; Williams, Evelyn W.; Zerega, Nyree J. C.

doi:10.3732/apps.1500049

Cited by 11 publications

(8 citation statements)

References 16 publications

(18 reference statements)

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“…Until now limited genomic information has been available for the Artocarpus genus as a whole. Microsatellite markers have been used to characterize cultivars and wild relatives of breadfruit [8,19,21,28], jackfruit [29], and other Artocarpus crop species [6,30,31]. Additionally, an assembled and annotated reference transcriptome of A. altilis has been generated [20].…”

Section: Introductionmentioning

confidence: 99%

Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Sahu

Ling

Yssel

et al. 2019

Genes

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Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

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Section: Introductionmentioning

confidence: 99%

Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Sahu

Ling

Yssel

et al. 2019

Genes

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show abstract

“…Until now only limited genomic information has been available for the Artocarpus genus as a whole. Microsatellite markers have been used to characterize cultivars and wild relatives of breadfruit [8,19,21,28], jackfruit [29], and other Artocarpus crop species [6,30,31].…”

Section: Introductionmentioning

confidence: 99%

Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Sahu¹,

Liu²,

Yssel

et al. 2019

Preprint

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Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 100 pounds). To date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2,822 and 2,034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch-and sucrose metabolism, photosynthesis and others. The copy number of several starch synthesis related genes were found increased in jackfruit and breadfruit compared to closely related species, and the tissue specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

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“…Existing genomic resources for breadfruit include nuclear ( Witherup et al, 2013 ) and chloroplast ( Gardner et al, 2015 ) microsatellites as well as transcriptomes of breadfruit and two wild relatives ( Laricchia, 2014 ). In this study, we augment these resources with a low-coverage shotgun assembly of the A. camansi genome.…”

mentioning

confidence: 99%

Low‐coverage, whole‐genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery

Gardner

Johnson²,

Ragone

et al. 2016

Appl Plant Sci

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Premise of the study:We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae.Methods and Results:A de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus.Conclusions:This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes.

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Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

Cited by 11 publications

References 16 publications

Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Low‐coverage, whole‐genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery

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