scholarly journals Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea

Biology ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 17
Author(s):  
Hua Yang ◽  
Philipp E. Bayer ◽  
Soodeh Tirnaz ◽  
David Edwards ◽  
Jacqueline Batley
Keyword(s):  
Brassica Juncea ◽  
Agronomic Traits ◽  
Gene Clusters ◽  
Gene Duplications ◽  
Genome Wide Analysis ◽  
Germplasm Resource ◽  
Genome Wide ◽  
Receptor Like Kinase ◽  
Development Processes ◽  
Allotetraploid Species

Brassica juncea, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in B. juncea. In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of B. juncea, using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between B. juncea and its progenitor species, B. rapa and B. nigra, indicate that 83.62% RLKs and 41.98% RLPs are conserved in B. juncea, and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.

scholarly journals A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 396 ◽  
Author(s):  
Trine B Rounge ◽  
Thomas Rohrlack ◽  
Alexander J Nederbragt ◽  
Tom Kristensen ◽  
Kjetill S Jakobsen
Keyword(s):  
Gene Clusters ◽  
Nonribosomal Peptide Synthetase ◽  
Nonribosomal Peptide ◽  
Genome Wide Analysis ◽  
Planktothrix Rubescens ◽  
Genome Wide ◽  
A Genome ◽  
Peptide Synthetase

scholarly journals Genomic insights into the origin, domestication and diversification of Brassica juncea

2021 ◽  
Vol 53 (9) ◽  
pp. 1392-1402
Author(s):  
Lei Kang ◽  
Lunwen Qian ◽  
Ming Zheng ◽  
Liyang Chen ◽  
Hao Chen ◽  
...  
Keyword(s):  
Brassica Juncea ◽  
De Novo ◽  
Gene Mutations ◽  
Sequencing Analysis ◽  
Genome Wide ◽  
Long Read ◽  
History Of ◽  
Crop Types ◽  
Allotetraploid Species ◽  
New Crop

AbstractDespite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000–14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.

Genome-wide analysis of the lectin receptor-like kinase family in foxtail millet (Setaria italica L.)

2016 ◽  
Vol 127 (2) ◽  
pp. 335-346 ◽  
Author(s):  
Wan Zhao ◽  
Yong-Wei Liu ◽  
Ji-Ming Zhou ◽  
Shu-Ping Zhao ◽  
Xiao-Hong Zhang ◽  
...  
Keyword(s):  
Foxtail Millet ◽  
Setaria Italica ◽  
Genome Wide Analysis ◽  
Lectin Receptor ◽  
Kinase Family ◽  
Genome Wide ◽  
Receptor Like Kinase

scholarly journals Genome-wide Identification and Analysis of CCT Genes in Wheat (Triticum Aestivum L.)

2020 ◽  
Author(s):  
Hongwei Zhang ◽  
Xinxia Liang ◽  
Shuo Zhou ◽  
Haibo Wang
Keyword(s):  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Suppressor Gene ◽  
Pcr Analysis ◽  
Genome Wide Analysis ◽  
Real Time Quantitative Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Mads Box Gene ◽  
And Function

Abstract Background: The vernalization, in which the plants must undergo a prolonged winter cold exposure to flower, is mainly controlled by a suppressive MADS-box gene FLC in Arabidopsis. However, different from Arabidopsis, the CCT-domain containing gene VRN2 is the critical vernalization-related suppressor gene in cereals. Based on this apparent diversity of vernalization in different plants, and involvement of VRN2 with vernalization in cereals, we conducted a genome-wide analysis of CCT genes in wheat, and the relationship between vernalization and these genes were also revealed.Results: A genome-wide analysis of the CCT genes in common wheat was performed by employing a hidden Markov model-based method, and 127 sequences, which assigned to 40 clusters, were obtained in three subgenomes. Specially, two of the gene clusters are duplicated, and distinguishingly located near telomere. Furthermore, these sequences were classified into eight groups by a phylogenetic analysis procedure using the UPGMA method, and this taxonomy is concordant to the classification based on CCT interruptions and domain organization which roughly divided the proteins into four divergently related subfamilies. Moreover, the expression of several CCT genes is continually downregulated during and after vernalization, but no continually upregulated CCT genes were revealed, as indicated by transcriptome sequencing and real-time quantitative PCR analysis.Conclusion: This study improves our understanding of the structure and function of CCT genes, suggests many vernalization-related CCT genes, and may guide future investigations on CCT genes and vernalization in wheat.

scholarly journals Genome-wide identification and transcriptional analyses of the R2R3-MYB gene family in wheat

2020 ◽  
Author(s):  
Chunsheng Xiao ◽  
Yong Jia ◽  
Calum Watt ◽  
Wenshuai Chen ◽  
Yujuan Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Agronomic Traits ◽  
Transcriptome Profiling ◽  
Segmental Duplications ◽  
Gene Duplications ◽  
Myb Gene ◽  
Homologous Genes ◽  
Genome Wide ◽  
Temporal And Spatial ◽  
R2r3 Myb

AbstractMYB transcription factors (TFs) represents one of the largest TF families in plants. In this study, we performed genome-wide MYB-domain screening and identified a total of 997 MYBs in wheat (Triticum aestivum), among which 445 were 2-domain MYBs (R2R3-MYBs) that were clustered into 15 subgroups with varied conservation profiles. Homologous genes were highly conserved across the three subgenomes, with minor variations contributed by segmental duplications. Tandem and proximal gene duplications have contributed significantly to the expansion of the wheat Myb gene family. Furthermore, comprehensive transcriptome profiling of R2R3-Myb genes in 61 different tissue and time point samples revealed a clear pattern of temporal and spatial variations within six expression groups. The comprehensive genomic and transcriptional analyses provided valuable insights into the evolution and biological functions of R2R3-Myb genes in wheat. They would serve as a useful guide to further investigate the potential agronomic traits controlled by this large TF family.

scholarly journals The transcriptional landscape of polyploid wheat

Science ◽  
2018 ◽  
Vol 361 (6403) ◽  
pp. eaar6089 ◽  
Author(s):  
R. H. Ramírez-González ◽  
P. Borrill ◽  
D. Lang ◽  
S. A. Harrington ◽  
J. Brinton ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Agronomic Traits ◽  
Expression Patterns ◽  
Polyploid Wheat ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Expression Atlas ◽  
Coordinated Expression ◽  
Coexpression Networks ◽  
Transcriptional Landscape

The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world’s major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.

scholarly journals A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4

2021 ◽  
Vol 37 (4) ◽  
pp. 389-395
Author(s):  
Da-Ran Kim ◽  
Youn-Sig Kwak
Keyword(s):  
Bacterial Species ◽  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Plant Diseases ◽  
Local Alignment ◽  
Plant Tissues ◽  
Biosynthetic Gene ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.

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