Plant DNA barcode library for native flowering plants in the arid region of northwestern China

Abstract

Arid regions, by definition, receive little precipitation (<25 cm of rain per year). They occupy about 35% of the Earth's land surface (Tchakerian, 2015). The Asian interior arid zone is the largest desert landform system in the Northern Hemisphere. In China, the arid region is concentrated in the northwest, including Xinjiang, the western region of Inner Mongolia, and Gansu, Ningxia and Qinghai provinces, with about 2.5 million km 2 or one-quarter of the entire Chinese territory (Wang et al., 2015). Northwest China is one of the driest regions in the world at this latitude. Most of the region has a temperate continental climate with low precipitation and a high drought frequency. It covers a climate gradient ranging from arid to hyperarid conditions with various desert habitats, including

Chloroplast genome‐based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions

“…For example, Song et al. ( 2023 ) included whole chloroplast genomes, along with traditional short Sanger‐based fragments, in a barcode library of the flowering plants of arid NW China while Krawczyk et al. ( 2018 ) used whole chloroplast genomes in a barcode library for the genus Stipa .…”

“…For example, the ability to cost‐effectively and reliably assemble the relatively small mitochondria of animals and chloroplast genome of plants using de novo or reference mapping methods from low‐coverage genome skimming data has accelerated our understanding of the variation in size, gene content and arrangement of these genomes (Li et al., 2020 ) with thousands of whole organelle genomes now available on GenBank. Whole mitochondria (De Mandal et al., 2014 ) and chloroplast (Song et al., 2023 ) genomes are now being incorporated into barcode libraries (called ultra‐barcodes) providing greater power to understand the phylogenetic affinity of taxa and increasing the ability to identify the small fragments of organelle DNA derived from ancient or environmental samples. The relatively low cost of genome skimming means that the whole organelle genome of multiple samples can feasibly be obtained, facilitating the discovery of potentially phylogenetically informative characters and mutational hotspots for the taxonomic level of interest (e.g.…”

Chloroplast genome-based genetic resources for Japan’s threatened subalpine forests via genome skimming

“…This is one of the first studies to develop ultra barcodes for species representing a distinct biome and contributes to an increasing trend to assemble whole chloroplast genomes for genetic resource development studies. For example, Song et al (2023) included whole chloroplast genomes, along with traditional short Sanger-based fragments, in a barcode library of the flowering plants of arid NW China while Krawczyk et al (2018) used whole chloroplast genomes in a barcode library for the genus Stipa. However, studies investigating within species variation of the whole chloroplast genome remain rare.…”

“…Whole mitochondria (De Mandal et al, 2014) and chloroplast (Song et al, 2023) genomes are now being incorporated into barcode libraries (called ultra barcodes) providing greater power to understand the phylogenetic affinity of taxa and increase the ability to identify the small fragments of organelle DNA derived from ancient or environmental samples. The relative low cost of genome skimming means that the whole organelle genome of multiple samples can feasibly be obtained, facilitating the discovery of potentially phylogenetically informative characters and mutational hotspots for the taxonomic level of interest (e.g.…”

“…For example, the ability to cost effectively and reliably assemble the relatively small mitochondria of animals and chloroplast genome of plants using de novo or reference mapping methods from low coverage genome skimming data has accelerated our understanding of the variation in size, gene content and arrangement of these genomes (Li et al ., 2020) with thousands of whole organelle genomes now available on Genbank. Whole mitochondria (De Mandal et al ., 2014) and chloroplast (Song et al ., 2023) genomes are now being incorporated into barcode libraries (called ultra barcodes) providing greater power to understand the phylogenetic affinity of taxa and increase the ability to identify the small fragments of organelle DNA derived from ancient or environmental samples. The relative low cost of genome skimming means that the whole organelle genome of multiple samples can feasibly be obtained, facilitating the discovery of potentially phylogenetically informative characters and mutational hotspots for the taxonomic level of interest (e.g.…”