4.7 Article

Resequencing of durian genomes reveals large genetic variations among different cultivars

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Plant Sciences

The pangenome of banana highlights differences between genera and genomes

Habib Rijzaani et al.

Summary: Banana from the Musaceae family has a complex genetic history, with different cultivated clones belonging to the Musa genus and Ensete species. The study presents the first cross-genus pangenome of banana, identifying genes that differentiate between species and potentially supporting breeding programs.

PLANT GENOME (2022)

Article Multidisciplinary Sciences

Genome wide study of cysteine rich receptor like proteins in Gossypium sp.

Athar Hussain et al.

Summary: This study conducted a comprehensive computational analysis of cysteine-rich receptor-like kinases (CRKs) in cotton and identified novel domains and miRNA target sites. The study also identified clusters of co-expression of CRKs under certain stress conditions. The results provide important data for understanding cotton adaptation to environmental stresses and serve as a reference for other economically important crops.

SCIENTIFIC REPORTS (2022)

Article Biotechnology & Applied Microbiology

Molecular diversity of exotic durian (Durio spp.) germplasm: a case study of Kalimantan, Indonesia

Dindin Hidayatul Mursyidin et al.

Summary: This study aimed to analyze the genetic diversity and relationship of exotic durian germplasm from Kalimantan, Indonesia. The results showed that the durian germplasm has low genetic diversity, but it exhibits unique relationships.

JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY (2022)

Article Biotechnology & Applied Microbiology

Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)

Cris Q. Cortaga et al.

Summary: This study analyzed the resistance gene analogs (RGAs) of durian and identified 2586 RGAs in its genome. These RGAs were functionally annotated and characterized through gene ontology (GO) analysis. The findings provide a valuable resource for genetic, agronomic, and other biological research of this important tropical fruit crop.

JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY (2022)

Article Biochemical Research Methods

Liftoff: accurate mapping of gene annotations

Alaina Shumate et al.

Summary: Advancements in DNA sequencing and computational methods have led to a significant increase in high-quality genome assemblies for many species. To annotate gene features in these genomes, a common strategy is to map genes from a previously annotated reference genome to new or improved assemblies. The tool Liftoff can accurately map genes between the same or closely related species, ensuring high sequence identity and preserving gene structure.

BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

OrthoDB in 2020: evolutionary and functional annotations of orthologs

Evgeny M. Zdobnov et al.

Summary: OrthoDB provides evolutionary and functional annotations of orthologs for a vast number of organisms, with a wide coverage of species and rich data content. The user interface has been enhanced, and features three views on the data, as well as online tools for interactive exploration and data download.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton

Maojun Wang et al.

Summary: Transposable element (TE) amplification plays a crucial role in mediating genome size expansion and evolution, with lineage-specific TE amplification contributing to large genome size differences in cotton species. The study also reveals changes in chromatin status in gene regions due to TE amplification and highlights the recent amplification of TEs affecting the formation of lineage-specific TAD boundaries in plants.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Plant Sciences

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper

Myung-Shin Kim et al.

Summary: The study presents de novo genome assemblies and annotations of Capsicum annuum 'Early Calwonder (non-pungent, ECW)' and 'Small Fruit (pungent, SF)', revealing a comprehensive analysis of their genetic structure and function, as well as significant regions of NLR gene copy number variation.

BMC PLANT BIOLOGY (2021)

Review Biotechnology & Applied Microbiology

How the pan-genome is changing crop genomics and improvement

Rafael Della Coletta et al.

Summary: Crop genomics has advanced significantly in recent years thanks to improvements in sequencing technology, assembly methods, and computational resources. The study of structural variation within species and the characterization of pan-genomes have revealed extensive genome content variation among individuals within a species, which is revolutionizing crop genomics and improvement.

GENOME BIOLOGY (2021)

Article Biochemistry & Molecular Biology

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

Diego Darriba et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Plant Sciences

Comparative genomics of six Juglans species reveals disease-associated gene family contractions

Alexander J. Trouern-Trend et al.

PLANT JOURNAL (2020)

Review Plant Sciences

Plant pangenomics: approaches, applications and advancements

Monica Furaste Danilevicz et al.

CURRENT OPINION IN PLANT BIOLOGY (2020)

Article Multidisciplinary Sciences

RepeatModeler2 for automated genomic discovery of transposable element families

Jullien M. Flynn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Genetics & Heredity

European maize genomes highlight intraspecies variation in repeat and gene content

Georg Haberer et al.

NATURE GENETICS (2020)

Article Biochemical Research Methods

CAFE 5 models variation in evolutionary rates among gene families

Fabio K. Mendes et al.

BIOINFORMATICS (2020)

Review Plant Sciences

Plant pan-genomes are the new reference

Philipp E. Bayer et al.

NATURE PLANTS (2020)

Article Biochemical Research Methods

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Alexey M. Kozlov et al.

BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis

Rainer Schwacke et al.

MOLECULAR PLANT (2019)

Article Plant Sciences

Recursive Paleohexaploidization Shaped the Durian Genome

Jinpeng Wang et al.

PLANT PHYSIOLOGY (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Wensheng Wang et al.

NATURE (2018)

Article Genetics & Heredity

The draft genome of tropical fruit durian (Durio zibethinus)

Bin Tean Teh et al.

NATURE GENETICS (2017)

Article Biochemical Research Methods

EUPAN enables pan-genome studies of a large number of eukaryotic genomes

Zhiqiang Hu et al.

BIOINFORMATICS (2017)

Article Biochemical Research Methods

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Mihaela Pertea et al.

NATURE PROTOCOLS (2016)

Article Multidisciplinary Sciences

The pangenome of an agronomically important crop plant Brassica oleracea

Agnieszka A. Golicz et al.

NATURE COMMUNICATIONS (2016)

Article Biochemical Research Methods

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

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Review Biochemistry & Molecular Biology

MYC2: The Master in Action

Kemal Kazan et al.

MOLECULAR PLANT (2013)

Article Plant Sciences

Isolation and characterization of ripening related pectin methylesterase inhibitor gene from banana fruit

Sudhakar Srivastava et al.

PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS (2012)

Article Biochemical Research Methods

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Carson Holt et al.

BMC BIOINFORMATICS (2011)

Review Biochemistry & Molecular Biology

The life and death of gene families

Jeffery P. Demuth et al.

BIOESSAYS (2009)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

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

David Ellinghaus et al.

BMC BIOINFORMATICS (2008)

Article Plant Sciences

A detached leaf bioassay to screen Durian cultivars for susceptibility to Phytophthora palmivora

LL Vawdrey et al.

AUSTRALASIAN PLANT PATHOLOGY (2005)

Article Biochemical Research Methods

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

RC Edgar

BMC BIOINFORMATICS (2004)

Article Biochemical Research Methods

Gene finding in novel genomes

I Korf

BMC BIOINFORMATICS (2004)