Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes

Abstract

Kobresia plants are important forage resources on the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants on the Qinghai-Tibetan Plateau. Previously, we have assembled the genome of Carex littledalei (Kobresia littledalei), which is a diploid with 29 chromosomes. In this study, we assembled genomes of Carex parvula (Kobresia pygmaea) and Carex kokanica (Kobresia royleana) via using Illumina and PacBio sequencing data, which were about 783.49 Mb and 673.40 Mb in size, respectively. And 45,002 or 36,709 protein-coding genes were further annotated in the genome of C. parvula or C. kokanica. Phylogenetic analysis indicated that Kobresia in Cyperaceae separated from Poaceae about 101.5 million years ago after separated from Ananas comosus in Bromeliaceae about 117.2 million years ago. C. littledalei and C. parvula separated about 5.0 million years ago, after separated from C. kokanica about 6.2 million years ago. In this study, transcriptome data of C. parvula at three different altitudes were also measured and analyzed. Kobresia plants genomes assembly and transcriptome analysis will assist research into mechanisms of plant adaptation to environments with high altitude and cold weather.

The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau

“… 56 Moreover, a consistent tendency for less proportion of LTR-RTs is possible in alpine sedges, for example, 27.87% ( K. littledalei ), 4 25.47% ( Carex parvula ), and 23.84% ( Carex kokanica ). 51 The reason for this pattern needs further investigation.…”

“…The genome of Kobresia littledalei provided by Can et al . 4 represents the first published chromosome-scale genome of sedge species (two draft genomes of K. pgymea and K. roylena 51 have also been published). The genome size of K. myosuroides is similar to that of K. littledalei (399.99 Mb vs. 373.85 Mb, respectively).…”

“…K. pygmea and K. littledalei diverged later (approximately 5.0 Mya). 4 , 51 Although the origin of Kobresia is assumed to be in the early Miocene (approximately 20 Mya), 58 they might have rapidly diversified during the late Miocene (23–5.3 Mya) to the Pliocene (5.3–2.6 Mya), a geological period thought to be critical for the speciation of Carex taxa 59 . Abundant uplift events have occurred in the QTP from the Miocene to the Pliocene, and rapid in situ diversification has been observed in several alpine lineages since the late Miocene.…”

Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus

“…More than 80 genomes have been published from species in the Poaceae, a member of Poales, an order with 14–16 families ( Bremer 2002 ; Bouchenak-Khelladi et al 2014 ; http://www.mobot.org/MOBOT/research/APweb/ ). Only 5 genomes have been sequenced from other species within Poales: 3 from Bromeliaceae, 1 from Typhaceae, and 3 from Cyperaceae ( Redwan et al 2016 ; Chen et al 2019 ; Can et al 2020 ; Liu et al 2021 ; Qu et al 2022 ; Widanagama et al 2022 ). Cyperaceae and Juncaceae are 2 sister families within Poales with about 5,000 and 440 species, respectively ( Goetghebeur 1998 ; Roalson 2005 ; Larridon et al 2021 ).…”

Genome Assembly and Microsatellite Marker Development Using Illumina and PacBio Sequencing in the Carex pumila (Cyperaceae) from Korea

“…In addition, genomic information can be used to facilitate drug discovery in medicinal plants [9]. So far, four genome assemblies of the Cyperaceae family have been reported: Kobresia littledalei, Carex parvula, Carex kokanica, and Kobresia myosuroides [10][11][12][13]. Currently, genomic information is continuously increasing, but it has been less compared to the number of species of Cyperaceae.…”