scholarly journals The emergence and evolution of intron‐poor and intronless genes in intron‐rich plant gene families

2020 ◽  
Author(s):  
Hui Liu ◽  
Hai‐Meng Lyu ◽  
Kaikai Zhu ◽  
Yves Van de Peer ◽  
Zong‐Ming (Max) Cheng
Keyword(s):  
Gene Families ◽  
Plant Gene ◽  
Intronless Genes

scholarly journals GeneHummus: A pipeline to define gene families and their expression in legumes and beyond

2018 ◽  
Author(s):  
Jose V. Die ◽  
Moamen Mahmoud Elmassry ◽  
Kimberly Hathaway LeBlanc ◽  
Olaitan I. Awe ◽  
Allissa Dillman ◽  
...  
Keyword(s):  
Large Scale ◽  
Rapid Development ◽  
High Specificity ◽  
Gene Families ◽  
Model Systems ◽  
Auxin Receptor ◽  
Plant Gene ◽  
Sequencing Technologies ◽  
Specificity And Sensitivity ◽  
The Impact

AbstractDuring the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called ‘orphan crops’) is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. Analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed and many gene families remain to be investigated. Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family, typically combining numerous BLAST searches and manually cleaning data. Due to the increasing abundance of genome sequences and the agronomical interest in plant gene families, the field needs a clear, automated annotation tool. Here, we present the GeneHummus pipeline, a step-by-step R-based pipeline for the identification, characterization and expression analysis of plant gene families. The impact of this pipeline comes from a reduction in hands-on annotation time combined with high specificity and sensitivity in extracting only proteins from the RefSeq database and providing the conserved domain architectures based on SPARCLE. As a case study we focused on the auxin receptor factors gene (ARF) family in Cicer arietinum (chickpea) and other legumes. We anticipate that our pipeline should be suitable for any plant gene family, and likely other gene families, vastly improving the speed and ease of genomic data processing.

Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure

2003 ◽  
pp. 111-116 ◽  
Author(s):  
Alain Lecharny ◽  
Nathalie Boudet ◽  
Isabelle Gy ◽  
Sébastien Aubourg ◽  
Martin Kreis
Keyword(s):  
Gene Structure ◽  
Gene Families ◽  
Plant Gene ◽  
Genomic Approach

Boost for conservation of plant gene assets

Nature ◽  
2009 ◽  
Author(s):  
Natasha Gilbert
Keyword(s):  
Plant Gene

An Overview of Plant Gene Regulation in Response to Salt Stress

2018 ◽  
Vol 26 ◽  
pp. 31-37
Author(s):  
Chan Young Jeong ◽  
Hojoung Lee
Keyword(s):  
Gene Regulation ◽  
Salt Stress ◽  
Plant Gene ◽  
Plant Gene Regulation

Identification of novel haplotype of a cyst nematode resistance gene, GmSNAP18 in soybean [Glycine max (L.) Merr.]

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
Ik-Young Choi ◽  
Prakash Basnet ◽  
Hana Yoo ◽  
Neha Samir Roy ◽  
Rahul Vasudeo Ramekar ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Gene Families ◽  
Nematode Resistance ◽  
Cyst Nematode ◽  
Soybean Breeding ◽  
Resistant Varieties ◽  
Soybean Genotypes ◽  
Glycine Max L ◽  
Scn Resistance

Soybean cyst nematode (SCN) is one of the most damaging pest of soybean. Discovery and characterization of the genes involved in SCN resistance are important in soybean breeding. Soluble NSF attachment protein (SNAP) genes are related to SCN resistance in soybean. SNAP genes include five gene families, and 2 haplotypes of exons 6 and 9 of SNAP18 are considered resistant to the SCN. In present study the haplotypes of GmSNAP18 were surveyed and chacterized in a total of 60 diverse soybean genotypes including Korean cultivars, landraces, and wild-types. The target region of exons 6 and 9 in GmSNAP18 region was amplified and sequenced to examine nucleotide variation. Characterization of 5 haplotypes identified in present study for the GmSNAP18 gene revealed two haplotypes as resistant, 1 as susceptible and two as novel. A total of twelve genotypes showed resistant haplotypes, and 45 cultivars were found susceptible. Interestingly, the two novel haplotypes were present in 3 soybean lines. The information provided here about the haplotypic variation of GmSNAP18 gene can be further explored for soybean breeding to develop resistant varieties.

Sign in / Sign up

Export Citation Format

Share Document