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Characterization of the first complete chloroplast genome of Amaranthus hybridus (Caryophyllales: Amaranthaceae) with phylogenetic implications.

ABSTRACT: In the present study, the complete chloroplast genome of Amaranthus hybridus was sequenced and assembled. The complete chloroplast genome of Amaranthus hybridus is 150,709 in size, with the GC content of 36.56%. The chloroplast genome of Amaranthus hybridus contained 86 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. Phylogenetic analysis based on combined chloroplast gene dataset indicated that the Amaranthus hybridus exhibited a close relationship with A. hypochondriacus and A. caudatus.

SUBMITTER: Bai X

PROVIDER: S-EPMC8555552 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Characterization of the first complete chloroplast genome of Amaranthus hybridus (Caryophyllales: Amaranthaceae) with phylogenetic implications.

Bai Xue X Ye Xueling X Luo Yiming Y Liu Changyin C Wu Qi Q

Mitochondrial DNA. Part B, Resources 20211027 11

In the present study, the complete chloroplast genome of Amaranthus hybridus was sequenced and assembled. The complete chloroplast genome of Amaranthus hybridus is 150,709 in size, with the GC content of 36.56%. The chloroplast genome of Amaranthus hybridus contained 86 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. Phylogenetic analysis based on combined chloroplast gene dataset indicated that the Amaranthus hybridus ...[more]

PMID: 34722881

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Project description:BackgroundThe genus Amaranthus L. consists of 70-80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically challenging and relationships among species including the dioecious ones are poorly understood. In this study, we investigated the phylogenetic relationships among the dioecious amaranths and sought to gain insights into plastid tree incongruence. A total of 19 Amaranthus species' complete plastomes were analyzed. Among these, seven dioecious Amaranthus plastomes were newly sequenced and assembled, an additional two were assembled from previously published short reads sequences and 10 other plastomes were obtained from a public repository (GenBank).ResultsComparative analysis of the dioecious Amaranthus species' plastomes revealed sizes ranged from 150,011 to 150,735 bp and consisted of 112 unique genes (78 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs). Maximum likelihood trees, Bayesian inference trees and splits graphs support the monophyly of subgenera Acnida (7 dioecious species) and Amaranthus; however, the relationship of A. australis and A. cannabinus to the other dioecious species in Acnida could not be established, as it appears a chloroplast capture occurred from the lineage leading to the Acnida + Amaranthus clades. Our results also revealed intraplastome conflict at some tree branches that were in some cases alleviated with the use of whole chloroplast genome alignment, indicating non-coding regions contribute valuable phylogenetic signals toward shallow relationship resolution. Furthermore, we report a very low evolutionary distance between A. palmeri and A. watsonii, indicating that these two species are more genetically related than previously reported.ConclusionsOur study provides valuable plastome resources as well as a framework for further evolutionary analyses of the entire Amaranthus genus as more species are sequenced.

Dataset Information

Characterization of the first complete chloroplast genome of Amaranthus hybridus (Caryophyllales: Amaranthaceae) with phylogenetic implications.

Publications

Characterization of the first complete chloroplast genome of <i>Amaranthus hybridus</i> (Caryophyllales: Amaranthaceae) with phylogenetic implications.

Similar Datasets

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