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

Delimitation of the new tribe Parartocarpeae (Moraceae) is supported by a 333-gene phylogeny and resolves tribal level Moraceae taxonomy

(2019) NYREE J.C. ZEREGA et al.   Phytotaxa

African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops

(2019) Prasad S. Hendre et al.   PLANTA

Genetic Diversity of Bangladeshi Jackfruit (Artocarpus heterophyllus) over Time and Across Seedling Sources

(2019) Colby Witherup et al.   ECONOMIC BOTANY

Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions

(2019) Rei Kajitani et al.   Nature Communications

Origin and diversity of an underutilized fruit tree crop, cempedak (Artocarpus integer , Moraceae)

(2018) Maria M. H. Wang et al.   AMERICAN JOURNAL OF BOTANY

A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.)

(2018) Kristen M. Laricchia et al.   AMERICAN JOURNAL OF BOTANY

A Flower in Fruit’s Clothing: Pollination of Jackfruit (Artocarpus heterophyllus, Moraceae) by a New Species of Gall Midge, Clinodiplosis ultracrepidata sp. nov. (Diptera: Cecidomyiidae)

(2018) Elliot M. Gardner et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

wgd—simple command line tools for the analysis of ancient whole-genome duplications

(2018) Arthur Zwaenepoel et al.   BIOINFORMATICS

The draft genomes of five agriculturally important African orphan crops

(2018) Yue Chang et al.   GigaScience

The draft genome of tropical fruit durian (Durio zibethinus)

(2017) Bin Tean Teh et al.   NATURE GENETICS

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

(2017) Michiel Van Bel et al.   NUCLEIC ACIDS RESEARCH

Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics

(2017) Yuling Lin et al.   GigaScience

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery

(2016) Elliot M. Gardner et al.   Applications in Plant Sciences

New Development and Validation of 50 SSR Markers in Breadfruit (Artocarpus altilis, Moraceae) by Next-Generation Sequencing

(2016) Fabien De Bellis et al.   Applications in Plant Sciences

Breadfruit (Artocarpus altilis): a source of high-quality protein for food security and novel food products

(2015) Ying Liu et al.   AMINO ACIDS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Diversity in the breadfruit complex (Artocarpus, Moraceae): genetic characterization of critical germplasm

(2015) Nyree Zerega et al.   Tree Genetics & Genomes

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

(2015) Zheng Chang et al.   GENOME BIOLOGY

Chloroplast Microsatellite Markers forArtocarpus(Moraceae) Developed from Transcriptome Sequences

(2015) Elliot M. Gardner et al.   Applications in Plant Sciences

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

The complex jujube genome provides insights into fruit tree biology

(2014) Meng-Jun Liu et al.   Nature Communications

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Identification of pro-vitamin A carotenoid-rich cultivars of breadfruit (Artocarpus, Moraceae)

(2013) A. Maxwell P. Jones et al.   JOURNAL OF FOOD COMPOSITION AND ANALYSIS

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Draft genome sequence of the mulberry tree Morus notabilis

(2013) Ningjia He et al.   Nature Communications

Development of Microsatellite Loci inArtocarpus altilis(Moraceae) and Cross-Amplification in Congeneric Species

(2013) Colby Witherup et al.   Applications in Plant Sciences

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Nutritional and morphological diversity of breadfruit (Artocarpus, Moraceae): Identification of elite cultivars for food security

(2011) A. Maxwell P. Jones et al.   JOURNAL OF FOOD COMPOSITION AND ANALYSIS

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

(2011) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Phylogeny and Recircumscription of Artocarpeae (Moraceae) with a Focus on Artocarpus

(2010) Nyree J. C. Zerega et al.   SYSTEMATIC BOTANY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

SMART 6: recent updates and new developments

(2008) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY