Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species

BMC Genomics
Bing-Hong HuangPei-Chun Liao

Abstract

Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species Zingiber kawagoii and Z. shuanglongensis was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of in situ ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses. Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in Z. kawagoii and no nucleotide substitution but only indels found in Z. shuanglongensis. Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species, Z. kawagoii and Z. shuanglongensis were estimated to be diverged since 21...Continue Reading

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Datasets Mentioned

BETA
MH758531-MH758541
PRJNA437070

Methods Mentioned

BETA
RNA-seq
environmental stresses
PCR

Software Mentioned

BLASTP
snpEff
bowtie2
MultiQC
bcftools
Trimmomatic
SnpSift
RSEM
FastQC
Trinity

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