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Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae)

Overview of attention for article published in BMC Genomics, November 2016
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Title
Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae)
Published in
BMC Genomics, November 2016
DOI 10.1186/s12864-016-3272-3
Pubmed ID
Authors

Catherine J. Nock, Abdul Baten, Bronwyn J. Barkla, Agnelo Furtado, Robert J. Henry, Graham J. King

Abstract

The large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes. Despite a long history of research, comparative analyses in the Proteaceae and macadamia breeding programs are restricted by a paucity of genetic information. To address this, we sequenced the genome and transcriptome of the widely grown Macadamia integrifolia cultivar 741. Over 95 gigabases of DNA and RNA-seq sequence data were de novo assembled and annotated. The draft assembly has a total length of 518 Mb and spans approximately 79% of the estimated genome size. Following annotation, 35,337 protein-coding genes were predicted of which over 90% were expressed in at least one of the leaf, shoot or flower tissues examined. Gene family comparisons with five other eudicot species revealed 13,689 clusters containing macadamia genes and 1005 macadamia-specific clusters, and provides evidence for linage-specific expansion of gene families involved in pathogen recognition, plant defense and monoterpene synthesis. Cyanogenesis is an important defense strategy in the Proteaceae, and a detailed analysis of macadamia gene homologues potentially involved in cyanogenic glycoside biosynthesis revealed several highly expressed candidate genes. The gene space of macadamia provides a foundation for comparative genomics, gene discovery and the acceleration of molecular-assisted breeding. This study presents the first available genomic resources for the large basal eudicot family Proteaceae, access to most macadamia genes and opportunities to uncover the genetic basis of traits of importance for adaptation and crop improvement.

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Mendeley readers

The data shown below were compiled from readership statistics for 40 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Italy 1 3%
Norway 1 3%
Unknown 38 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 10 25%
Student > Master 7 18%
Student > Doctoral Student 5 13%
Student > Ph. D. Student 4 10%
Professor 4 10%
Other 4 10%
Unknown 6 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 24 60%
Biochemistry, Genetics and Molecular Biology 5 13%
Arts and Humanities 1 3%
Environmental Science 1 3%
Computer Science 1 3%
Other 1 3%
Unknown 7 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 22 November 2016.
All research outputs
#4,646,734
of 8,670,160 outputs
Outputs from BMC Genomics
#3,820
of 6,068 outputs
Outputs of similar age
#159,792
of 296,878 outputs
Outputs of similar age from BMC Genomics
#108
of 217 outputs
Altmetric has tracked 8,670,160 research outputs across all sources so far. This one is in the 46th percentile – i.e., 46% of other outputs scored the same or lower than it.
So far Altmetric has tracked 6,068 research outputs from this source. They receive a mean Attention Score of 4.2. This one is in the 36th percentile – i.e., 36% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 296,878 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 45th percentile – i.e., 45% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 217 others from the same source and published within six weeks on either side of this one. This one is in the 49th percentile – i.e., 49% of its contemporaries scored the same or lower than it.