Research Advances and Prospects in Charophytes Genomics

doi:10.11983/CBB24083

Abstract

Abstract: Charophytes and land plants form a monophyletic group known as Streptophyta. Fossil and molecular evidences suggest that land plants originated from charophytes. This article summarizes the 14 sequenced genomes of 10 species in charophytes and reviews the molecular mechanisms involved in the terrestrialization of plants, revealing the genomic basis for the pre-adaptation of charophytes that included the expansion of gene families regulating plant hormone signal transduction and encoding key transcription factors, as well as horizontal gene transfer. We elucidate with examples the helpful role of the whole-genome data of charophytes in transcriptomic and functional genomic discovery. Moreover, we discuss the importance of telomere-to-telomere genomes and pan-genomes for a deeper understanding of plant terrestrialization and the future directions of integrating genomic data with biological experiments for deciphering the function and origin of charophyte genes.

Key words: charophytes, evolutionary comparative genomics, genome, terrestrialization

Linfeng Xia, Rui Li, Haizheng Wang, Daling Feng, Chunyang Wang. Research Advances and Prospects in Charophytes Genomics[J]. Chinese Bulletin of Botany, 2025, 60(2): 271-282.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24083

https://www.chinbullbotany.com/EN/Y2025/V60/I2/271

Figures/Tables 4

References 58

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Species	Class	Order	Family
Zygnema circumcarinatum	Zygnematophyceae	Zygnematales	Zygnemataceae
Z. cf. cylindricum	Zygnematophyceae	Zygnematales	Zygnemataceae
Mesotaenium endlicherianum	Zygnematophyceae	Zygnematales	Mesotaeniaceae
Spirogloea muscicola	Zygnematophyceae	Spirogloeales	Spirogloeaceae
Closterium peracerosum-strigosum-littorale complex	Zygnematophyceae	Desmidiales	Closteriaceae
Penium margaritaceum	Zygnematophyceae	Desmidiales	Peniaceae
Chara braunii	Charophyceae	Charales	Characeae
Klebsormidium nitens	Klebsormidiophyceae	Klebsormidiales	Klebsormidiaceae
Chlorokybus atmophyticus	Chlorokybophyceae	Chlorokybales	Chlorokybaceae
Mesostigma viride	Mesostigmatophyceae	Mesostigmatales	Mesostigmataceae

Species	Class	Order	Family
Zygnema circumcarinatum	Zygnematophyceae	Zygnematales	Zygnemataceae
Z. cf. cylindricum	Zygnematophyceae	Zygnematales	Zygnemataceae
Mesotaenium endlicherianum	Zygnematophyceae	Zygnematales	Mesotaeniaceae
Spirogloea muscicola	Zygnematophyceae	Spirogloeales	Spirogloeaceae
Closterium peracerosum-strigosum-littorale complex	Zygnematophyceae	Desmidiales	Closteriaceae
Penium margaritaceum	Zygnematophyceae	Desmidiales	Peniaceae
Chara braunii	Charophyceae	Charales	Characeae
Klebsormidium nitens	Klebsormidiophyceae	Klebsormidiales	Klebsormidiaceae
Chlorokybus atmophyticus	Chlorokybophyceae	Chlorokybales	Chlorokybaceae
Mesostigma viride	Mesostigmatophyceae	Mesostigmatales	Mesostigmataceae

Species (strain)	Predicted genome size (Mb)	Assembly size (Mb)	Number of scaffold	Scaffold N50 (kb)	GC content (%)	Number of gene	Reference
Zygnema circumcarinatum (SAG 698-1b)	66.7	71.0	90 (20)	3958.3	50.0	16617	Feng et al., 2024
Z. circumcarinatum (UTEX 1559)	66.3	71.3	614	3970.3	49.5	18062	Feng et al., 2024
Z. circumcarinatum (UTEX 1560)	67.8	67.3	514	3792.7	49.5	18654	Feng et al., 2024
Z. cf. cylindricum (SAG 698-1a_XF)	322.5	359.8	3587	213.9	40.0	45178	Feng et al., 2024
Mesotaenium endlicherianum (SAG 12.97)	163.0	173.8	13942	448.4	52.0	11080	Cheng et al., 2019
Spirogloea muscicola (CCAC 0214)	174.0	171.1	19678	566	56.5	27137	Cheng et al., 2019
Closterium peracerosum-strigosum-littorale complex (NIES-67)	365.0	360.0	NA	351*	56.1	29752	Sekimoto et al., 2023
C. peracerosum-strigosum-littorale complex (NIES-68)	361.0	337.0	NA	275*	55.8	28427	Sekimoto et al., 2023
Penium margaritaceum (SAG 2640)	4700.0	3661.0	332786	116.1	51.0	52333	Jiao et al., 2020

Species (strain)	Predicted genome size (Mb)	Assembly size (Mb)	Number of scaffold	Scaffold N50 (kb)	GC content (%)	Number of gene	Reference
Zygnema circumcarinatum (SAG 698-1b)	66.7	71.0	90 (20)	3958.3	50.0	16617	Feng et al., 2024
Z. circumcarinatum (UTEX 1559)	66.3	71.3	614	3970.3	49.5	18062	Feng et al., 2024
Z. circumcarinatum (UTEX 1560)	67.8	67.3	514	3792.7	49.5	18654	Feng et al., 2024
Z. cf. cylindricum (SAG 698-1a_XF)	322.5	359.8	3587	213.9	40.0	45178	Feng et al., 2024
Mesotaenium endlicherianum (SAG 12.97)	163.0	173.8	13942	448.4	52.0	11080	Cheng et al., 2019
Spirogloea muscicola (CCAC 0214)	174.0	171.1	19678	566	56.5	27137	Cheng et al., 2019
Closterium peracerosum-strigosum-littorale complex (NIES-67)	365.0	360.0	NA	351*	56.1	29752	Sekimoto et al., 2023
C. peracerosum-strigosum-littorale complex (NIES-68)	361.0	337.0	NA	275*	55.8	28427	Sekimoto et al., 2023
Penium margaritaceum (SAG 2640)	4700.0	3661.0	332786	116.1	51.0	52333	Jiao et al., 2020

Species (strain)	Predicting genome size (Mb)	Assembly size (Mb)	Number of scaffold	Scaffold N50 (kb)	GC content (%)	Number of gene	Reference
Chara braunii (S276)	2355.0	1751.5	11654	2260	48.3	23546	Nishiyama et al., 2018
Klebsormidium nitens (NIES-2285)	117.1±21.8	104.0	1812	134.9	52.4	16215	Hori et al., 2014
Chlorokybus atmophyticus (CCAC 0220)	85.0	74.0	3836	752.4	51.5	9066	Wang et al., 2020
Mesostigma viride (CCAC 1140)	329.0	281.0	6924	113.2	55.0	9198	Wang et al., 2020
M. viride (NIES-296)	NA	442.6	2363	2558.7	54.5	24431	Liang et al., 2019