Analysis of Whole Genome Characteristics of Helianthus annuus

Longkuiza 6 Chloroplast

Jun Ma

Instiitude of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Xuefu Street, Harbin, Heilongjiang, China

Keywords: Helianthus annuus, Chloroplast Genome, Characteristics.

Abstract: The whole chloroplast genome was assembled and annotated on the leaf high-throughput sequencing data of

the oil sunflower hybrid longkuiza 6. The results showed that the whole chloroplast genome was 151124bp

in length, including a typical tetrad structure. Two single-copy regions were separated by a pair of inverted

repeat regions. The lengths of LSC and SSC were 83548bp and 18308bp, respectively. The chloroplast

genome encodes a total of 127 genes, including 84 protein-coding genes, 8 rRNA genes and 35 tRNA genes.

In the chloroplast genome of Helianthus annuus longkuiza 6, there are a total of 18 genes containing introns,

except for the ycf3 and clpP genes, the rest contain 1 intron. In the protein coding gene of H. annuus longkuiza

6, leucine is the amino acid with the highest codon encoding rate, and the amino acid with the lowest encoding

rate is cysteine.

1 INTRODUCTION

The chloroplast genome contains a large number of

functional genes, which have important research

value in species identification and system evolution

(Dong 2021, Gao 2019) The chloroplast genome

exists in a covalently closed double-stranded form

and consists of four regions: a pair of inverted repeat

regions, a large single-copy sequence region, and a

small single-copy sequence region (Wen 2021,

Redwan 2015). Chloroplast genome sequence has the

characteristics of highly conservative, stable

structure, slow molecular evolution rate and small

molecular weight, which makes it play an important

role in cytoplasmic inheritance, plant phylogeny,

development of DNA barcode, genetic diversity and

genetic relationship (Ng 2017, Coombe 2016).

Therefore, the chloroplast genome has become one of

the most effective tools for studying plant phylogeny.

Helianthus annuus belongs to the Asteraceae

Helianthus is an annual herbaceous plant and is an

important oil crop (Liu 2020, Hussain 2017). Wild

sunflower gradually evolved into cultivated

sunflower after long-term natural selection and

artificial domestication. This study analyzed the

whole genome of the chloroplast of H. annuus

https://orcid.org/0000-0002-3287-9940

longkuiza 6, hoping to provide a reference for the

classification, evolutionary analysis and utilization of

resources.

2 MATERIALS AND METHODS

2.1 Experimental Materials

The H. annuus longkuiza 6 was selected for the

experiment. The experimental materials were

provided by the Economic Crop Research Institute of

Heilongjiang Academy of Agricultural Sciences.

During the experiment, fresh sunflower leaves were

collected for follow-up experiments.

2.2 DNA Extraction and

High-throughput Sequencing

Collect H. annuus longkuiza 6 samples, clean the

surface of the leaves, extract the total DNA of H.

annuus longkuiza 6 leaves with the CTAB method,

and detect the concentration and purity by 1%

agarose gel electrophoresis and UV

spectrophotometer. The qualified samples were

Ma, J.

Analysis of Whole Genome Characteristics of Helianthus annuus Longkuiza 6 Chloroplast.

DOI: 10.5220/0011294400003443

In Proceedings of the 4th Inter national Conference on Biomedical Engineering and Bioinformatics (ICBEB 2022), pages 749-752

ISBN: 978-989-758-595-1

749

commissioned by BGI for high-throughput

sequencing of H. annuus longkuiza 6 genome.

2.3 Assembly and Annotation of

Chloroplast Genome

Filter the original data to obtain high-quality data.

Use BLAT software to position and compare it with

the chloroplast reference genome of closely related

species, obtain the relative position between contig

sequences, and correct assembly errors to obtain the

full-length cpDNA framework. After that, use

GapCloser software to fill high-quality short

sequences into the gaps on the frame diagram

sequence, and use first-generation sequencing to

supplement and confirm the remaining gaps and

suspicious regions. The H. annuus longkuiza 6

cpDNA was annotated by CPGAVAS2, a special

annotation software for chloroplasts, and the

annotated results were graphed and analyzed by

OGDRAW software.

3 RESULTS AND DISCUSSION

3.1 H. annuus Longkuiza 6 Chloroplast

Genome Structure and Gene

Annotation

The assembled and spliced H. annuus longkuiza 6

chloroplast genome has a full length of 151124 bp

and a GC content of 38%. It has a highly conservative

and typical tetrad structure. The large single copy

fragment (LSC) has a length of 83548bp, the small

single copy fragment (SSC) has a length of 18308bp,

and a pair of inverted repeat fragments (IRa and IRb)

has a length of 24634bp. A total of 127 genes were

annotated in the chloroplast genome sequence of H.

annuus longkuiza 6, including 84 protein-coding

genes, 35 tRNA genes and 8 rRNA genes (Table 1).

The 84 protein-coding genes can be divided into three

broad categories. The first category is self-

replication-related genes, the second category is

photosynthesis-related genes, and the third category

is other protein-coding genes and genes with

unknown functions.

The IR region contains 34 genes, which are 12

protein-coding genes (2 rpl2, 2 rpl23, 2 ycf2, 2 ndhB,

2 rps7, 2 rps12), 14 tRNA genes (2 trnI-CAU, 2 trnI-

GAU, 2 trnL-CAA, 2 trnV-GAC, 2 trnA, 2 trnR-ACG,

2 trnN-GUU), and 8 ribosomal RNA genes (2 rrn16s,

2 rrn23s, 2 rrn4.5s, 2 rrn5s) (Figure 1). The rps12

gene is a split gene, the 5'end is located in the LSC

region, and the 3'end is located in the two IR regions.

Table 1: Basic characteristics of H. annuus longkuiza 6

chloroplasts

Chloro

lasts feature Numerical value

Len

(

151124

GC content (%) 38

AT content

(

)

LSC length (bp) 83548

SSC len

(

18308

IR length (bp) 24634

Gene numbe

127

Gene number in IR

regions

Protein-coding gene

numbe

Protein-codin

ene

(

)

66.14

rRNA gene numbe

rRNA

(

)

6.30

tRNA gene numbe

tRNA

(

)

27.56

Figure 1: Gene cycle graph of the H. annuus longkuiza 6

chloroplast genome

3.2 Analysis of Introns and Exons of H.

annuus Longkuiza 6 Chloroplast

Genome

H. annuus longkuiza 6 chloroplast genome contains

18 genes containing introns, including 12 CDS and 6

tRNA. The ycf3 and clpP genes contain 2 introns, and

the other genes contain only one intron. In addition,

the intron of ndhA is the longest at 1084 bp, and the

intron of trnL-UAA is the shortest at 437 bp (Table 2).

ICBEB 2022 - The International Conference on Biomedical Engineering and Bioinformatics

750

Table 2: Genes with introns and exons of H. annuus longkuiza 6 chloroplast genome.

Gene Start En

Exon I Intron I Exon II Intron II Exon III

5216 6351 40 869 227

rpoC1 16304 19105 432 732 1638

27079 28346 145 713 410

ycf3 42284 44234 124 699 230 745 153

trnL-UAA 47045 47566 38 437 47

trn

-UA

50816 51463 38 573 37

69365 71327 71 751 294 621 226

petB 74278 75699 6 774 642

etD 75894 77087 8 711 475

rpl2 83705 85194 391 665 434

ndhB 93287 95489 777 670 756

trn

-GAU 101028 101878 42 774 35

trnA 101943 102836 38 822 34

ndhA 114693 116868 553 1084 539

trnA 131839 132732 38 822 34

trn

-GAU 132797 133647 42 774 35

ndhB 139186 141388 777 670 756

rpl2 149481 150970 391 665 434

3.3 Codon Preference of H. annuus

Longkuiza 6 Chloroplast Genome

In the H. annuus longkuiza 6 chloroplast genome, the

most codon-encoded amino acid is leucine Leu, with

5111 (accounting for 10.58%); the least codon-

encoded amino acid is cysteine Cys, with 537

(accounting for 1.11%). Among these codons, the

most used codon is ATT, which encodes isoleucine

Ile and occurs 1950 times, and the least used is TGC,

which encodes Cys and 151 times. Except for

tryptophan Trp and methionine Met, which have only

one codon, the rest of the amino acids have 2-6

codons.

Table 3: Codon Usage in the chloroplast genome of H.annuus longkuiza 6.

Amino acid Codon Numbe

Val (V)

GTA

GTC

GTG

GTT

897

345

347

912

Met (M) TTC

ATG

986

1159

Gln (Q)

CAA

CAG

1291

446

Tyr (Y)

TAT

TAC

1482

338

Lys (K) AAG

AAA

723

1901

Cys (C) TGT

TGC

386

151

Trp (W)

TGG 882 Leu (L)

CTT

CTG

CTA

CTC

TTA

TTG

1115

322

691

329

1530

1124

Asp (D)

GAT

GAC

1558

407

Thr (T)

ACT

ACA

ACG

ACC

980

716

239

428

Ile (I)

ATC

ATA

ATT

827

1269

1950

Asn (N)

AAC

AAT

552

1829

Ser (S)

AGC

AGT

TCG

TCA

TCC

TCT

248

754

325

753

566

1068

His (H)

CAT

CAC

849

292

Arg (R)

AGG

AGA

CGA

CGC

CGG

CGT

335

889

628

188

233

641

Pro (P)

CCT

CCG

CCA

CCC

731

328

580

370

Gly (G)

GGT

GGG

GGA

GGC

1037

554

1236

363

Ala (A)

GCA

GCC

GCG

GCT

766

396

281

1165

Phe (F)

TTT 1826 Glu (E)

GAG

GAA

629

1839

Terminator TAG

TGA

TAA

145

Analysis of Whole Genome Characteristics of Helianthus annuus Longkuiza 6 Chloroplast

751

4 CONCLUSIONS

In this paper, the structural characteristics of the

whole chloroplast genome of H. annuus longkuiza 6

are studied. The results show that it is similar to the

chloroplast genome structure of most plants. It has a

highly conserved four-region structure, including a

pair of 24634 bp inverted repeat regions (IR), a large

single copy region (LSC) of 83548 bp and a small

single copy region (SSC) of 18308 bp. H. annuus

longkuiza 6 has annotated a total of 127 genes,

including 84 protein-coding genes, 8 rRNA genes and

35 tRNA genes. There are 18 genes with introns, of

which the rps12 gene has a trans-spliced intron. The

study of the whole genome structure and sequence

information of the chloroplast of H. annuus longkuiza

6 laid the foundation for the study of its genetic

background and the exploration of the relationship

between system evolution. Using the chloroplast

structural genome characteristics to explore can

provide a basis for the relationship between

sunflower phylogeny and evolution, and provide

reference value for the future development,

utilization and molecular evolution of primers for

Helianthus plants.

ACKNOWLEDGEMENT

The Heilongjiang Provincial Government

Postdoctoral Funding (Grant Number LBH-Z17204).

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