Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses

Abstract

The genus Allium is one of the largest monocotyledonous genera, containing over 850 species, and most of these species are found in temperate climates of the Northern Hemisphere. Furthermore, as a large number of new Allium species continue to be identified, phylogenetic classification based on morphological characteristics and a few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present the use of complete chloroplast genome sequences in genome-scale phylogenetic studies of Allium . We sequenced and assembled four Allium chloroplast genomes and retrieved five published chloroplast genomes from GenBank. All nine chloroplast genomes were used for genomic comparison and phylogenetic inference. The chloroplast genomes, ranging from 152,387 bp to 154,482 bp in length, exhibited conservation of genomic structure, and gene organization and order. Subsequently, we observed the expansion of IRs from the basal monocot Acorus americanus to Allium , identified 814 simple sequence repeats, 131 tandem repeats, 154 dispersed repeats and 109 palindromic repeats, and found six highly variable regions. The phylogenetic relationships of the Allium species inferred from the chloroplast genomes obtained high support, indicating that chloroplast genome data will be useful for further resolution of the phylogeny of the genus Allium .

Complete chloroplast genomes of Zingiber montanum and Zingiber zerumbet: Genome structure, comparative and phylogenetic analyses

“…The chloroplast genome sequences provided useful genomic resources for phylogenetic studies [51,52]. Several previous studies have successfully used protein-coding genes, whole chloroplast genome sequences, or chloroplast SNP-based matrices for phylogenetic inference in the family Zingiberaceae [13,[15][16][17][18][19][20][21][22][23][24][25][26].…”

Taxonomy and biogeography ofDiapensia(Diapensiaceae) based on chloroplast genome data

“…Generation of plastid genome sequences has become relatively easy and inexpensive by Genome Skimming for evolutionary studies (Wen et al, 2018;Yan et al, 2018;Li et al, 2019;Liu et al, 2019;Rabah et al, 2019;Valcárcel & Wen, 2019). As a result, chloroplast (cp) genome data have recently been widely used for plant phylogenetic studies and are useful to resolve relationships at various taxonomic levels, including species delimitation (e.g., Jansen et al, 2006;Yang et al, 2013;Huang et al, 2016;Niu et al, 2018;Fu et al 2019;Huo et al, 2019;Zhang et al, 2019). Here, we sequenced the complete plastid genomes of 15 species (including one variety and two forms) of Diapensiaceae.…”

Omics approaches inAlliumresearch: Progress and way ahead

“…Therefore, the chloroplast genome is widely used for phylogeny and diversity analyses in plants. The chloroplast genome of several Allium species have been characterized using NGS platforms ( Filyushin et al, 2018 ; Xie et al, 2019a ; Yusupov et al, 2019 ) and used for marker discovery ( Lee et al, 2017 ; Kim, Park & Yang, 2015 ) , phylogenetic analyses ( Xie et al, 2019b ; Huo et al, 2019 ) , and the study of male sterility ( Von Kohn, Kiełkowska & Havey, 2013 ; Kim, Park & Yang, 2015 ; Table 1 ). The complete chloroplast genome is 152,387–154,482 bp in length,with a GC content of 36%–37% ( Filyushin et al, 2016 ; Lee et al, 2017 ; Xie et al, 2019a ; Xie et al, 2019b ; Yusupov et al, 2019 ) .…”

“…The number of genes in this genome ranges from 114 to 141. Repeat analyses revealed that all chloroplast genomes contain similar repeat sequences ( Huo et al, 2019 ) . Information generated from chloroplast genome sequencing could be harnessed for studying and improving Allium crops.…”