Chaney Lindsay, Mangelson Ryan, Ramaraj Thiruvarangan, Jellen Eric N, Maughan Peter J
Department of Plant and Wildlife Sciences, Brigham Young University, 5144 Life Sciences Building, Provo, Utah 84602 USA.
The National Center for Genomic Resources, Santa Fe, New Mexico 87505 USA.
Appl Plant Sci. 2016 Sep 19;4(9). doi: 10.3732/apps.1600063. eCollection 2016 Sep.
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.
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.
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.
苋属包含许多重要的谷物和杂草物种。我们通过开发完整的参考叶绿体基因组来加深对该属的理解。
利用长读长技术开发了高质量的皱果苋（苋科）叶绿体基因组组装。该参考基因组用于重建两个近缘谷物物种（尾穗苋和千穗谷）及其假定祖先（杂种苋）的叶绿体基因组。参考基因组为150,518 bp，具有环状结构，由小单拷贝区（17,941 bp）和大单拷贝区（83,873 bp）分隔的两个反向重复序列（24,352 bp）；它编码111个基因，其中72个为蛋白质编码基因。相对于参考叶绿体基因组，在分析的基因组中平均鉴定出210个单核苷酸多态性（SNP）和122个插入/缺失多态性（indel）。
该参考叶绿体基因组，连同已报道的简单序列重复、SNP和indel，是研究苋属植物系统发育和遗传多样性的宝贵遗传资源。
