NDLI: Molecular evolution of a family of resistance gene analogs of nucleotide-binding site sequences in Solanum lycopersicum

Content Provider	Springer Nature Link
Author	Liao, Pei Chun Lin, Kuan Hung Ko, Chin Ling Hwang, Shih Ying
Copyright Year	2011
Abstract	Nucleotide-binding site-leucine-rich repeats (NBS-LRR) gene families are one of the major plant resistance genes. Genomic NBS evolution was studied in many plant species for diverse arrays of NBS gene families. In this study, we focused on one family of NBS sequences in an attempt to understand how closely related NBS sequences evolved in the light of selection in domesticated plant species. A phylogenetic analysis revealed five major clades (A–E) and five subclades (A1–A5) within clade A of cloned NBS sequences. Positive selection was only detected in newly evolved NBS lineages in subclades of clade A. Positively selected codon sites were found among NBS sequences of clade A. A sliding-window analysis revealed that regions with Ka/Ks ratios of >1 were in the inter-motifs when paired clades were compared, but regions with Ka/Ks ratios of >1 were found across NBS sequences when subclades of clade A were compared. Our results based on a family of closely related NBS sequences showed that positive selection was first exerted on specific lineages across all NBS sequences after selective constraints. Subsequently, sequences with mutations in commonly conserved motifs were scrutinized by purifying selection. In the long term, conserved high frequency alleles in commonly conserved motifs and changes in inter-motifs were maintained in the investigated family of NBS sequences. Moreover, codons identified to be under positive selection in the inter-motifs were mainly located in regions involved in functions of ATP binding or hydrolysis.
Starting Page	1229
Ending Page	1240
Page Count	12
File Format	PDF
ISSN	00166707
Journal	Genetica
Volume Number	139
Issue Number	10
e-ISSN	15736857
Language	English
Publisher	Springer Netherlands
Publisher Date	2011-12-28
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	NBS sequences Positive selection Resistance gene analogs Solanum lycopersicum Plant Genetics & Genomics Human Genetics Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Medicine Animal Science and Zoology Insect Science

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