z-logo
Premium
Genome‐wide characterization and expression analysis of genetic variants in sweet orange
Author(s) -
Jiao WenBiao,
Huang Ding,
Xing Feng,
Hu Yibo,
Deng XiuXin,
Xu Qiang,
Chen LingLing
Publication year - 2013
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12254
Subject(s) - biology , genome , genetics , loss of heterozygosity , indel , gene , contig , ploidy , single nucleotide polymorphism , allele , genotype
Summary Heterozyosity is an important feature of many plant genomes, and is related to heterosis. Sweet orange, a highly heterozygous species, is thought to have originated from an inter‐species hybrid between pummelo and mandarin. To investigate the heterozygosity of the sweet orange genome and examine how this heterozygosity affects gene expression, we characterized the genome of V alencia orange for single nucleotide variations ( SNV s), small insertions and deletions ( I n D els) and structural variations ( SV s), and determined their functional effects on protein‐coding genes and non‐coding sequences. Almost half of the genes containing large‐effect SNV s and I n D els were expressed in a tissue‐specific manner. We identified 3542 large SV s (>50 bp), including deletions, insertions and inversions. Most of the 296 genes located in large‐deletion regions showed low expression levels. RNA ‐ S eq reads and DNA sequencing reads revealed that the alleles of 1062 genes were differentially expressed. In addition, we detected approximately 42 Mb of contigs that were not found in the reference genome of a haploid sweet orange by de novo assembly of unmapped reads, and annotated 134 protein‐coding genes within these contigs. We discuss how this heterozygosity affects the quality of genome assembly. This study advances our understanding of the genome architecture of sweet orange, and provides a global view of gene expression at heterozygous loci.

This content is not available in your region!

Continue researching here.

Having issues? You can contact us here