
The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)
Author(s) -
Chaney Lindsay,
Mangelson Ryan,
Ramaraj Thiruvarangan,
Jellen Eric N.,
Maughan Peter J.
Publication year - 2016
Publication title -
applications in plant sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.64
H-Index - 23
ISSN - 2168-0450
DOI - 10.3732/apps.1600063
Subject(s) - biology , genome , amaranthus hypochondriacus , indel , amaranthus hybridus , genetics , inverted repeat , reference genome , whole genome sequencing , amaranthus cruentus , chloroplast dna , genus , evolutionary biology , single nucleotide polymorphism , amaranth , gene , botany , genotype , weed , agronomy
Premise of the study: The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. Methods and Results: A high‐quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long‐read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species ( A. cruentus and A. caudatus ) and their putative progenitor ( A. hybridus ). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single‐copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single‐nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes. Conclusions: This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.