The genome assembly and annotation of<i>Magnolia biondii</i>Pamp., a phylogenetically, economically, and medicinally important ornamental tree species
Abstract Magnolia biondiiPamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Contributing a genome sequence forM. biondiiwill help resolve phylogenetic uncertainty of magnoliids and further understand individual trait evolution inMagnolia. We assembled a chromosome-level reference genome ofM. biondiiusing ~67, ~175, and ~154 Gb of raw DNA sequences generated by Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ⍰2.22 Gb with a contig N50 of 269.11 Kb and a BUSCO complete gene ratio of 91.90%. About 89.17% of the genome length was organized to 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 48,319 protein-coding genes, accounting for 22.97% of the genome length, in contrast to 66.48% of the genome length for the repetitive elements. We confirmed a Magnoliaceae specific WGD event that might have probably occurred shortly after the split of Magnoliaceae and Annonaceae. Functional enrichment of theMagnoliaspecific and expanded gene families highlighted genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, and response to stimulus, which may improve ecological fitness and biological adaptability of the lineage. Phylogenomic analyses recovered a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence ofM. biondiicould empower trait improvement, germplasm conservation, and evolutionary studies on rapid radiation of early angiosperms..
| Medienart: |
|
|---|
Preprint| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
bioRxiv.org - (2023) vom: 02. Okt. Zur Gesamtaufnahme - year:2023 |
|---|
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Dong, Shanshan [VerfasserIn] |
|---|
| Links: |
Volltext [kostenfrei] |
|---|
| Themen: |
|---|
| doi: |
10.1101/2020.06.17.158428 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
XBI01817910X |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | XBI01817910X | ||
| 003 | DE-627 | ||
| 005 | 20231005090801.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 200622s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1101/2020.06.17.158428 |2 doi | |
| 035 | |a (DE-627)XBI01817910X | ||
| 035 | |a (biorXiv)10.1101/2020.06.17.158428 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Dong, Shanshan |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a The genome assembly and annotation of<i>Magnolia biondii</i>Pamp., a phylogenetically, economically, and medicinally important ornamental tree species |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 520 | |a Abstract Magnolia biondiiPamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Contributing a genome sequence forM. biondiiwill help resolve phylogenetic uncertainty of magnoliids and further understand individual trait evolution inMagnolia. We assembled a chromosome-level reference genome ofM. biondiiusing ~67, ~175, and ~154 Gb of raw DNA sequences generated by Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ⍰2.22 Gb with a contig N50 of 269.11 Kb and a BUSCO complete gene ratio of 91.90%. About 89.17% of the genome length was organized to 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 48,319 protein-coding genes, accounting for 22.97% of the genome length, in contrast to 66.48% of the genome length for the repetitive elements. We confirmed a Magnoliaceae specific WGD event that might have probably occurred shortly after the split of Magnoliaceae and Annonaceae. Functional enrichment of theMagnoliaspecific and expanded gene families highlighted genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, and response to stimulus, which may improve ecological fitness and biological adaptability of the lineage. Phylogenomic analyses recovered a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence ofM. biondiicould empower trait improvement, germplasm conservation, and evolutionary studies on rapid radiation of early angiosperms. | ||
| 650 | 4 | |a Biology |7 (dpeaa)DE-84 | |
| 650 | 4 | |a 570 |7 (dpeaa)DE-84 | |
| 700 | 1 | |a Liu, Min |4 aut | |
| 700 | 1 | |a Liu, Yang |4 aut | |
| 700 | 1 | |a Chen, Fei |4 aut | |
| 700 | 1 | |a Yang, Ting |4 aut | |
| 700 | 1 | |a Chen, Lu |4 aut | |
| 700 | 1 | |a Zhang, Xingtan |4 aut | |
| 700 | 1 | |a Guo, Xing |4 aut | |
| 700 | 1 | |a Fang, Dongming |4 aut | |
| 700 | 1 | |a Li, Linzhou |4 aut | |
| 700 | 1 | |a Deng, Tian |4 aut | |
| 700 | 1 | |a Yao, Zhangxiu |4 aut | |
| 700 | 1 | |a Lang, Xiaoan |4 aut | |
| 700 | 1 | |a Gong, Yiqing |4 aut | |
| 700 | 1 | |a Wu, Ernest |4 aut | |
| 700 | 1 | |a Wang, Yaling |4 aut | |
| 700 | 1 | |a Shen, Yamei |4 aut | |
| 700 | 1 | |a Gong, Xun |4 aut | |
| 700 | 1 | |a Liu, Huan |4 aut | |
| 700 | 1 | |a Zhang, Shouzhou |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t bioRxiv.org |g (2023) vom: 02. Okt. |
| 773 | 1 | 8 | |g year:2023 |g day:02 |g month:10 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1101/2020.06.17.158428 |z kostenfrei |3 Volltext |
| 912 | |a GBV_XBI | ||
| 951 | |a AR | ||
| 952 | |j 2023 |b 02 |c 10 | ||